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 882 patients, 691 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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, 691 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
17p gain	196 (22%)	686	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0308 (0.0454)	0.00071 (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)
20q gain	237 (27%)	645	0.0356 (0.0519)	0.0496 (0.0707)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0097 (0.0152)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0001 (0.000208)	1e-05 (2.35e-05)	0.00854 (0.0135)	0.00014 (0.000286)
3p loss	411 (47%)	471	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0006 (0.00113)	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)
9p loss	192 (22%)	690	0.017 (0.026)	0.0211 (0.0318)	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 (4.44e-05)	0.0001 (0.000208)
9q loss	195 (22%)	687	0.0383 (0.0556)	0.0388 (0.0563)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	4e-05 (8.63e-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 (4.44e-05)	8e-05 (0.000169)
14q loss	265 (30%)	617	5e-05 (0.000107)	0.0001 (0.000208)	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)
3p gain	103 (12%)	779	0.00157 (0.00276)	0.00749 (0.0119)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.211 (0.266)	0.00702 (0.0112)	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)
3q gain	161 (18%)	721	0.0184 (0.0279)	0.0475 (0.0679)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.34 (0.403)	0.00289 (0.00489)	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	252 (29%)	630	0.0313 (0.046)	0.0644 (0.0893)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0292 (0.0433)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	4e-05 (8.63e-05)	1e-05 (2.35e-05)	0.00024 (0.000481)	1e-05 (2.35e-05)
12q gain	256 (29%)	626	0.0308 (0.0454)	0.0629 (0.0878)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0117 (0.0181)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.0003 (0.000593)	1e-05 (2.35e-05)
17q gain	222 (25%)	660	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.152 (0.197)	0.00338 (0.00562)	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)
xp gain	129 (15%)	753	0.011 (0.017)	0.0089 (0.014)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.291 (0.353)	0.00222 (0.00381)	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)
xq gain	130 (15%)	752	0.00023 (0.000462)	0.00056 (0.00106)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.633 (0.689)	0.00438 (0.00718)	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)
1p loss	145 (16%)	737	0.00313 (0.00526)	0.0131 (0.0202)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.357 (0.42)	3e-05 (6.56e-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)
1q loss	110 (12%)	772	0.0188 (0.0284)	0.0137 (0.0211)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.79 (0.84)	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)
2p loss	65 (7%)	817	1e-05 (2.35e-05)	0.00041 (0.00079)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.14 (0.182)	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)
2q loss	63 (7%)	819	0.00018 (0.000364)	6e-05 (0.000128)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.324 (0.387)	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)
6p loss	171 (19%)	711	0.00633 (0.0102)	0.00356 (0.00591)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0008 (0.00147)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.155 (0.201)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
6q loss	206 (23%)	676	0.00822 (0.013)	0.00358 (0.00593)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00213 (0.00368)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.67 (0.727)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
13q loss	137 (16%)	745	0.00652 (0.0104)	0.0113 (0.0176)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.0759 (0.104)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00164 (0.00288)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
17p loss	111 (13%)	771	0.00206 (0.00356)	0.00311 (0.00523)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.586 (0.643)	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	82 (9%)	800	0.00034 (0.000666)	0.00036 (0.000704)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.623 (0.68)	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)
21q loss	133 (15%)	749	0.0263 (0.0391)	0.0241 (0.0361)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.957 (0.992)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.44e-05)	1e-05 (2.35e-05)
22q loss	107 (12%)	775	0.00721 (0.0115)	0.0375 (0.0545)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.339 (0.402)	7e-05 (0.000148)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.00032 (0.00063)	3e-05 (6.56e-05)
xp loss	114 (13%)	768	0.0297 (0.0439)	0.0307 (0.0453)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.53 (0.595)	0.00014 (0.000286)	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)
1q gain	68 (8%)	814	0.601 (0.658)	0.695 (0.749)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00307 (0.00518)	0.0276 (0.041)	0.00021 (0.000423)	1e-05 (2.35e-05)	0.0031 (0.00522)	1e-05 (2.35e-05)	0.0342 (0.0502)	1e-05 (2.35e-05)
5p gain	238 (27%)	644	0.486 (0.549)	0.603 (0.66)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0344 (0.0503)	7e-05 (0.000148)	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)
7p gain	369 (42%)	513	0.118 (0.157)	0.11 (0.147)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0101 (0.0158)	0.00194 (0.00337)	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)
7q gain	371 (42%)	511	0.119 (0.158)	0.109 (0.146)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0142 (0.0218)	0.00117 (0.00208)	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	103 (12%)	779	0.0976 (0.131)	0.243 (0.3)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00605 (0.00973)	0.00019 (0.000384)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0255 (0.0381)	1e-05 (2.35e-05)	0.0014 (0.00247)	4e-05 (8.63e-05)
16p gain	281 (32%)	601	0.0826 (0.112)	0.0681 (0.0941)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00518 (0.00842)	0.00049 (0.000933)	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)
16q gain	268 (30%)	614	0.0887 (0.12)	0.0573 (0.0809)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00285 (0.00484)	0.00037 (0.000715)	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)
20p gain	233 (26%)	649	0.0632 (0.0879)	0.0763 (0.104)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0183 (0.0278)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	9e-05 (0.000189)	1e-05 (2.35e-05)	0.00687 (0.011)	0.00012 (0.000249)
4p loss	98 (11%)	784	0.491 (0.554)	0.48 (0.543)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0256 (0.0382)	4e-05 (8.63e-05)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.00069 (0.00128)	1e-05 (2.35e-05)	0.00102 (0.00183)	0.00012 (0.000249)
18p loss	141 (16%)	741	0.3 (0.363)	0.408 (0.474)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0004 (0.000772)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00189 (0.00329)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	8e-05 (0.000169)
18q loss	148 (17%)	734	0.227 (0.282)	0.353 (0.417)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00072 (0.00133)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00817 (0.0129)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
4p gain	47 (5%)	835	0.196 (0.249)	0.42 (0.486)	0.00029 (0.000575)	1e-05 (2.35e-05)	0.538 (0.602)	0.00092 (0.00168)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
4q gain	46 (5%)	836	0.365 (0.428)	0.649 (0.705)	0.00043 (0.000823)	1e-05 (2.35e-05)	0.54 (0.603)	0.0033 (0.0055)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
5q gain	253 (29%)	629	0.16 (0.206)	0.207 (0.262)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.568 (0.63)	3e-05 (6.56e-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 gain	39 (4%)	843	0.758 (0.811)	0.743 (0.797)	0.00055 (0.00104)	1e-05 (2.35e-05)	0.744 (0.797)	0.00257 (0.00438)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00095 (0.00172)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
3q loss	119 (13%)	763	0.139 (0.182)	0.139 (0.182)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.888 (0.934)	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)	5e-05 (0.000107)	0.00104 (0.00187)
4q loss	92 (10%)	790	0.502 (0.565)	0.624 (0.68)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.152 (0.197)	5e-05 (0.000107)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.0029 (0.0049)	1e-05 (2.35e-05)	0.00321 (0.00538)	4e-05 (8.63e-05)
5p loss	24 (3%)	858			0.00017 (0.000346)	1e-05 (2.35e-05)	0.0433 (0.0623)	0.0447 (0.0643)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.066 (0.0912)	1e-05 (2.35e-05)	0.00063 (0.00118)	6e-05 (0.000128)
10p loss	133 (15%)	749	0.378 (0.44)	0.358 (0.421)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.57 (0.632)	6e-05 (0.000128)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00037 (0.000715)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
xq loss	113 (13%)	769	0.0619 (0.0865)	0.0559 (0.0792)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.697 (0.75)	3e-05 (6.56e-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)
1p gain	31 (4%)	851	0.87 (0.919)	0.915 (0.956)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.00031 (0.000611)	0.00075 (0.00138)	0.00601 (0.00968)	1e-05 (2.35e-05)	0.266 (0.327)	1e-05 (2.35e-05)	0.0642 (0.0892)	0.0102 (0.0158)
2q gain	127 (14%)	755	0.459 (0.525)	0.327 (0.39)	1e-05 (2.35e-05)	0.00029 (0.000575)	0.523 (0.587)	0.00599 (0.00966)	0.00326 (0.00545)	1e-05 (2.35e-05)	0.191 (0.243)	0.00078 (0.00144)	0.0201 (0.0304)	0.00206 (0.00356)
8p gain	69 (8%)	813	0.365 (0.428)	0.471 (0.536)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.222 (0.277)	0.00037 (0.000715)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.201 (0.255)	1e-05 (2.35e-05)	0.00081 (0.00148)	0.00056 (0.00106)
15q gain	52 (6%)	830	0.873 (0.921)	0.556 (0.619)	0.00044 (0.000841)	1e-05 (2.35e-05)	0.898 (0.941)	0.0312 (0.0459)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.232 (0.288)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
19p gain	74 (8%)	808	0.196 (0.249)	0.217 (0.272)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.177 (0.227)	0.0022 (0.00378)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.5 (0.564)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
19q gain	78 (9%)	804	0.0653 (0.0903)	0.0645 (0.0894)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0619 (0.0865)	0.00037 (0.000715)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.195 (0.248)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
5q loss	23 (3%)	859			2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.149 (0.194)	0.0512 (0.0727)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0261 (0.0389)	1e-05 (2.35e-05)	0.00037 (0.000715)	6e-05 (0.000128)
8p loss	161 (18%)	721	0.133 (0.174)	0.276 (0.338)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.596 (0.654)	0.128 (0.17)	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 loss	83 (9%)	799	0.353 (0.417)	0.504 (0.567)	0.00069 (0.00128)	2e-05 (4.44e-05)	0.289 (0.353)	0.876 (0.923)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00984 (0.0154)	0.00013 (0.000267)	0.00115 (0.00205)	0.00092 (0.00168)
10q loss	157 (18%)	725	0.277 (0.339)	0.238 (0.294)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.428 (0.495)	0.0009 (0.00165)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.119 (0.158)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
11q loss	52 (6%)	830	0.177 (0.227)	0.304 (0.366)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.577 (0.636)	0.0024 (0.0041)	0.00011 (0.000229)	1e-05 (2.35e-05)	0.12 (0.158)	0.00016 (0.000326)	2e-05 (4.44e-05)	0.00033 (0.000648)
15q loss	68 (8%)	814	0.25 (0.308)	0.269 (0.33)	2e-05 (4.44e-05)	1e-05 (2.35e-05)	0.184 (0.235)	0.00043 (0.000823)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0975 (0.131)	0.00146 (0.00257)	0.00391 (0.00643)	0.0022 (0.00378)
16p loss	18 (2%)	864			0.539 (0.602)	0.00378 (0.00623)	0.225 (0.28)	0.0094 (0.0147)	0.00027 (0.00054)	0.00062 (0.00116)	0.034 (0.0499)	0.00479 (0.00783)	0.00014 (0.000286)	0.00397 (0.00652)
2p gain	120 (14%)	762	0.46 (0.525)	0.33 (0.392)	1e-05 (2.35e-05)	0.00106 (0.0019)	0.484 (0.547)	0.0174 (0.0265)	0.00244 (0.00416)	2e-05 (4.44e-05)	0.0894 (0.121)	0.00188 (0.00329)	0.0517 (0.0735)	0.00203 (0.00352)
9q gain	24 (3%)	858			0.0485 (0.0692)	1e-05 (2.35e-05)	0.771 (0.823)	0.284 (0.347)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.318 (0.38)	1e-05 (2.35e-05)	0.0005 (0.00095)	0.00013 (0.000267)
11p gain	58 (7%)	824	0.355 (0.418)	0.812 (0.86)	0.00119 (0.00211)	2e-05 (4.44e-05)	0.436 (0.501)	0.0793 (0.108)	3e-05 (6.56e-05)	1e-05 (2.35e-05)	0.21 (0.265)	1e-05 (2.35e-05)	0.00013 (0.000267)	1e-05 (2.35e-05)
11q gain	55 (6%)	827	0.476 (0.539)	0.914 (0.956)	0.00238 (0.00407)	1e-05 (2.35e-05)	0.69 (0.745)	0.548 (0.612)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.161 (0.208)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
18p gain	54 (6%)	828	0.574 (0.634)	0.749 (0.802)	0.435 (0.501)	2e-05 (4.44e-05)	0.788 (0.839)	0.356 (0.419)	3e-05 (6.56e-05)	0.00018 (0.000364)	0.0232 (0.0349)	2e-05 (4.44e-05)	0.00095 (0.00172)	0.00099 (0.00179)
18q gain	50 (6%)	832	0.64 (0.696)	0.774 (0.825)	0.579 (0.638)	1e-05 (2.35e-05)	0.687 (0.743)	0.291 (0.353)	4e-05 (8.63e-05)	1e-05 (2.35e-05)	0.0452 (0.0648)	1e-05 (2.35e-05)	0.0003 (0.000593)	3e-05 (6.56e-05)
22q gain	64 (7%)	818	0.37 (0.432)	0.467 (0.533)	0.00029 (0.000575)	1e-05 (2.35e-05)	0.894 (0.939)	0.16 (0.206)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.929 (0.969)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
11p loss	42 (5%)	840	0.059 (0.0829)	0.0713 (0.0982)	0.00515 (0.00839)	9e-05 (0.000189)	0.572 (0.632)	0.158 (0.205)	0.00094 (0.00171)	2e-05 (4.44e-05)	0.113 (0.15)	0.001 (0.0018)	2e-05 (4.44e-05)	0.00185 (0.00324)
16q loss	28 (3%)	854			0.0215 (0.0323)	0.00046 (0.000877)	0.151 (0.196)	0.213 (0.267)	0.00664 (0.0106)	0.00059 (0.00111)	0.0789 (0.108)	0.00114 (0.00203)	0.00111 (0.00199)	0.00866 (0.0136)
19q loss	23 (3%)	859			0.00363 (0.006)	0.00096 (0.00174)	0.693 (0.748)	0.309 (0.371)	0.00215 (0.00371)	0.00071 (0.00132)	0.00465 (0.00761)	0.0403 (0.0583)	0.00145 (0.00256)	0.0828 (0.112)
9p gain	26 (3%)	856	0.0579 (0.0816)	0.0723 (0.0994)	0.141 (0.183)	1e-05 (2.35e-05)	0.725 (0.779)	0.556 (0.619)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.325 (0.387)	1e-05 (2.35e-05)	0.00066 (0.00123)	0.00037 (0.000715)
19p loss	29 (3%)	853			0.00112 (0.002)	0.00029 (0.000575)	0.374 (0.436)	0.0631 (0.0879)	0.00059 (0.00111)	0.00022 (0.000443)	0.131 (0.172)	0.0235 (0.0353)	0.00081 (0.00148)	0.112 (0.149)
20p loss	12 (1%)	870			0.936 (0.975)	0.00714 (0.0114)	0.204 (0.258)	0.199 (0.252)	0.00043 (0.000823)	0.014 (0.0215)	0.536 (0.601)	0.00378 (0.00623)	0.00598 (0.00966)	0.0138 (0.0213)
20q loss	6 (1%)	876			0.584 (0.643)	0.00497 (0.00811)	0.249 (0.307)	0.437 (0.503)	0.00272 (0.00462)	0.0145 (0.0222)	1 (1.00)	0.00585 (0.00947)	0.00866 (0.0136)	0.00581 (0.00942)
13q gain	52 (6%)	830	0.221 (0.275)	0.297 (0.36)	0.00331 (0.00551)	0.0972 (0.131)	0.346 (0.41)	0.302 (0.364)	0.0345 (0.0504)	0.0179 (0.0273)	0.0371 (0.0539)	0.015 (0.023)	0.298 (0.361)	0.211 (0.266)
21q gain	72 (8%)	810	0.444 (0.51)	0.453 (0.519)	1e-05 (2.35e-05)	0.0498 (0.071)	0.301 (0.363)	0.0203 (0.0307)	0.00013 (0.000267)	0.00132 (0.00234)	0.0566 (0.08)	0.132 (0.173)	0.944 (0.981)	0.954 (0.99)
6p gain	22 (2%)	860			0.397 (0.462)	0.129 (0.171)	0.0462 (0.0662)	0.0906 (0.122)	0.943 (0.981)	0.0109 (0.017)	0.433 (0.5)	0.0741 (0.102)	0.00189 (0.00329)	0.0253 (0.0378)
10p gain	28 (3%)	854	0.195 (0.248)	0.421 (0.488)	0.0183 (0.0278)	0.183 (0.234)	0.225 (0.28)	0.106 (0.143)	0.00322 (0.00539)	0.00574 (0.00932)	0.47 (0.535)	0.00812 (0.0129)	0.219 (0.274)	0.47 (0.535)
10q gain	22 (2%)	860	0.0391 (0.0565)	0.118 (0.157)	0.0583 (0.082)	0.801 (0.85)	0.317 (0.38)	0.576 (0.636)	0.058 (0.0816)	0.0787 (0.108)	0.759 (0.811)	0.0592 (0.0829)	0.884 (0.931)	0.802 (0.851)
7p loss	4 (0%)	878			0.683 (0.74)	0.13 (0.171)	0.571 (0.632)	0.041 (0.0592)	0.214 (0.268)	0.3 (0.363)	0.279 (0.341)	0.174 (0.224)	0.0839 (0.114)	0.373 (0.436)
7q loss	4 (0%)	878			0.685 (0.741)	0.13 (0.171)	0.571 (0.632)	0.0418 (0.0602)	0.217 (0.271)	0.302 (0.364)	0.276 (0.339)	0.175 (0.224)	0.084 (0.114)	0.371 (0.434)
6q gain	16 (2%)	866			0.623 (0.68)	0.401 (0.466)	0.103 (0.138)	0.312 (0.374)	0.863 (0.912)	0.159 (0.205)	0.851 (0.9)	0.309 (0.371)	0.0725 (0.0997)	0.45 (0.516)
12p loss	7 (1%)	875			0.895 (0.939)	0.248 (0.306)	0.342 (0.404)	0.913 (0.956)	0.954 (0.99)	0.557 (0.619)	0.797 (0.847)	0.434 (0.501)	0.0533 (0.0756)	0.279 (0.341)
12q loss	4 (0%)	878			1 (1.00)		0.471 (0.536)	0.473 (0.537)	0.333 (0.395)	0.683 (0.74)	0.221 (0.275)	0.713 (0.767)

'1p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
1P GAIN MUTATED	5	1	25
1P GAIN WILD-TYPE	323	199	329

Figure S1. 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 = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
1P GAIN MUTATED	3	8	0	9	0
1P GAIN WILD-TYPE	99	115	171	61	186

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00061

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
1P GAIN MUTATED	12	2	1	12
1P GAIN WILD-TYPE	170	179	186	185

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0014

Table S4. Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
1P GAIN MUTATED	2	0	8	3	5	1	8
1P GAIN WILD-TYPE	195	64	108	144	54	70	85

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.0097

Table S5. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
1P GAIN MUTATED	4	15	5	6
1P GAIN WILD-TYPE	118	184	280	267

Figure S5. 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 = 2.4e-05

Table S6. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
1P GAIN MUTATED	1	5	1	4	11	5	3	0	0
1P GAIN WILD-TYPE	87	56	147	80	110	33	108	59	169

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
1P GAIN MUTATED	1	28	2	0
1P GAIN WILD-TYPE	75	319	231	208

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
1P GAIN MUTATED	0	7	0	0	3	1	1
1P GAIN WILD-TYPE	91	76	49	20	43	76	45

Figure S8. 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 = 2.4e-05

Table S9. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
1Q GAIN MUTATED	7	4	57
1Q GAIN WILD-TYPE	321	196	297

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S10. Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
1Q GAIN MUTATED	2	15	6	16	3
1Q GAIN WILD-TYPE	100	108	165	54	183

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0052

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
1Q GAIN MUTATED	16	8	8	26
1Q GAIN WILD-TYPE	166	173	179	171

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

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.041

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
1Q GAIN MUTATED	11	1	10	12	9	3	12
1Q GAIN WILD-TYPE	186	63	106	135	50	68	81

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00042

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
1Q GAIN MUTATED	4	30	18	14
1Q GAIN WILD-TYPE	118	169	267	259

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
1Q GAIN MUTATED	0	8	11	11	20	7	6	3	0
1Q GAIN WILD-TYPE	88	53	137	73	101	31	105	56	169

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0031 (Fisher's exact test), Q value = 0.0052

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
1Q GAIN MUTATED	14	17	35
1Q GAIN WILD-TYPE	328	177	293

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
1Q GAIN MUTATED	0	52	13	1
1Q GAIN WILD-TYPE	76	295	220	207

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

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.05

Table S17. Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
1Q GAIN MUTATED	5	3	9	7
1Q GAIN WILD-TYPE	151	66	56	115

Figure S17. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S18. Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
1Q GAIN MUTATED	2	17	0	0	3	2	0
1Q GAIN WILD-TYPE	89	66	49	20	43	75	46

Figure S18. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
2P GAIN MUTATED	37	1	82
2P GAIN WILD-TYPE	291	199	272

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0019

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
2P GAIN MUTATED	4	14	23	18	27
2P GAIN WILD-TYPE	98	109	148	52	159

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
2P GAIN MUTATED	18	3	17	23	14	11	16
2P GAIN WILD-TYPE	179	61	99	124	45	60	77

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.0042

Table S22. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
2P GAIN MUTATED	6	38	38	37
2P GAIN WILD-TYPE	116	161	247	236

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S23. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
2P GAIN MUTATED	1	12	18	7	30	4	18	2	27
2P GAIN WILD-TYPE	87	49	130	77	91	34	93	57	142

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.0033

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
2P GAIN MUTATED	1	51	37	31
2P GAIN WILD-TYPE	75	296	196	177

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.0035

Table S25. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
2P GAIN MUTATED	15	17	3	0	11	8	1
2P GAIN WILD-TYPE	76	66	46	20	35	69	45

Figure S25. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S26. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
2Q GAIN MUTATED	41	2	84
2Q GAIN WILD-TYPE	287	198	270

Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
2Q GAIN MUTATED	4	13	25	19	31
2Q GAIN WILD-TYPE	98	110	146	51	155

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

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00599 (Fisher's exact test), Q value = 0.0097

Table S28. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
2Q GAIN MUTATED	18	3	17	26	14	12	18
2Q GAIN WILD-TYPE	179	61	99	121	45	59	75

Figure S28. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0054

Table S29. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
2Q GAIN MUTATED	6	37	42	42
2Q GAIN WILD-TYPE	116	162	243	231

Figure S29. 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 = 2.4e-05

Table S30. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
2Q GAIN MUTATED	1	12	18	8	29	5	21	2	31
2Q GAIN WILD-TYPE	87	49	130	76	92	33	90	57	138

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0014

Table S31. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
2Q GAIN MUTATED	1	52	39	34
2Q GAIN WILD-TYPE	75	295	194	174

Figure S31. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.03

Table S32. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
2Q GAIN MUTATED	24	3	14	20
2Q GAIN WILD-TYPE	132	66	51	102

Figure S32. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0036

Table S33. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
2Q GAIN MUTATED	16	19	5	0	11	9	1
2Q GAIN WILD-TYPE	75	64	44	20	35	68	45

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0028

Table S34. Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
3P GAIN MUTATED	0	2	2	6
3P GAIN WILD-TYPE	31	23	11	11

Figure S34. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.012

Table S35. Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S35. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S36. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
3P GAIN MUTATED	90	1	12
3P GAIN WILD-TYPE	238	199	342

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S37. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
3P GAIN MUTATED	12	12	1	4	59
3P GAIN WILD-TYPE	90	111	170	66	127

Figure S37. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.011

Table S38. Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
3P GAIN MUTATED	17	10	20	14	4	12	3
3P GAIN WILD-TYPE	180	54	96	133	55	59	90

Figure S38. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
3P GAIN MUTATED	15	11	2	75
3P GAIN WILD-TYPE	107	188	283	198

Figure S39. 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 = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
3P GAIN MUTATED	13	8	1	7	6	2	2	0	64
3P GAIN WILD-TYPE	75	53	147	77	115	36	109	59	105

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

'3p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
3P GAIN MUTATED	88	9	6
3P GAIN WILD-TYPE	254	185	322

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

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
3P GAIN MUTATED	11	22	2	68
3P GAIN WILD-TYPE	65	325	231	140

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

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S43. Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
3P GAIN MUTATED	46	8	7	3
3P GAIN WILD-TYPE	110	61	58	119

Figure S43. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S44. Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
3P GAIN MUTATED	29	8	17	0	2	1	7
3P GAIN WILD-TYPE	62	75	32	20	44	76	39

Figure S44. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.028

Table S45. Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
3Q GAIN MUTATED	1	6	2	6
3Q GAIN WILD-TYPE	30	19	11	11

Figure S45. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.068

Table S46. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S46. 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 = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
3Q GAIN MUTATED	107	4	50
3Q GAIN WILD-TYPE	221	196	304

Figure S47. 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 = 2.4e-05

Table S48. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
3Q GAIN MUTATED	12	23	7	13	75
3Q GAIN WILD-TYPE	90	100	164	57	111

Figure S48. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.0049

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
3Q GAIN MUTATED	28	12	36	20	10	15	10
3Q GAIN WILD-TYPE	169	52	80	127	49	56	83

Figure S49. 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 = 2.4e-05

Table S50. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
3Q GAIN MUTATED	16	36	13	96
3Q GAIN WILD-TYPE	106	163	272	177

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S51. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
3Q GAIN MUTATED	13	12	8	13	25	6	5	3	76
3Q GAIN WILD-TYPE	75	49	140	71	96	32	106	56	93

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
3Q GAIN MUTATED	106	29	25
3Q GAIN WILD-TYPE	236	165	303

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

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
3Q GAIN MUTATED	11	55	11	83
3Q GAIN WILD-TYPE	65	292	222	125

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

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
3Q GAIN MUTATED	59	8	13	9
3Q GAIN WILD-TYPE	97	61	52	113

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

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S55. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
3Q GAIN MUTATED	39	18	16	0	6	3	7
3Q GAIN WILD-TYPE	52	65	33	20	40	74	39

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

'4p gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

Table S56. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
4P GAIN MUTATED	30	3	14
4P GAIN WILD-TYPE	298	197	340

Figure S56. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
4P GAIN MUTATED	25	4	1	2	5
4P GAIN WILD-TYPE	77	119	170	68	181

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

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0017

Table S58. Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
4P GAIN MUTATED	13	5	14	1	2	2	2
4P GAIN WILD-TYPE	184	59	102	146	57	69	91

Figure S58. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S59. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
4P GAIN MUTATED	27	8	3	8
4P GAIN WILD-TYPE	95	191	282	265

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S60. Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
4P GAIN MUTATED	27	5	0	3	5	1	0	1	4
4P GAIN WILD-TYPE	61	56	148	81	116	37	111	58	165

Figure S60. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S61. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
4P GAIN MUTATED	35	5	7
4P GAIN WILD-TYPE	307	189	321

Figure S61. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S62. Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
4P GAIN MUTATED	27	11	3	6
4P GAIN WILD-TYPE	49	336	230	202

Figure S62. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S63. Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
4P GAIN MUTATED	5	21	3	2
4P GAIN WILD-TYPE	151	48	62	120

Figure S63. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S64. Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
4P GAIN MUTATED	4	2	1	1	2	1	20
4P GAIN WILD-TYPE	87	81	48	19	44	76	26

Figure S64. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00082

Table S65. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
4Q GAIN MUTATED	29	3	14
4Q GAIN WILD-TYPE	299	197	340

Figure S65. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S66. Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
4Q GAIN MUTATED	25	3	2	2	5
4Q GAIN WILD-TYPE	77	120	169	68	181

Figure S66. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.0055

Table S67. Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
4Q GAIN MUTATED	13	5	13	1	2	2	3
4Q GAIN WILD-TYPE	184	59	103	146	57	69	90

Figure S67. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S68. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
4Q GAIN MUTATED	27	7	4	7
4Q GAIN WILD-TYPE	95	192	281	266

Figure S68. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
4Q GAIN MUTATED	27	4	0	2	5	1	1	1	4
4Q GAIN WILD-TYPE	61	57	148	82	116	37	110	58	165

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

'4q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S70. Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
4Q GAIN MUTATED	34	5	7
4Q GAIN WILD-TYPE	308	189	321

Figure S70. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S71. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
4Q GAIN MUTATED	27	9	4	6
4Q GAIN WILD-TYPE	49	338	229	202

Figure S71. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S72. Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
4Q GAIN MUTATED	5	21	2	2
4Q GAIN WILD-TYPE	151	48	63	120

Figure S72. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S73. Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
4Q GAIN MUTATED	4	1	1	1	2	1	20
4Q GAIN WILD-TYPE	87	82	48	19	44	76	26

Figure S73. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S74. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
5P GAIN MUTATED	40	26	172
5P GAIN WILD-TYPE	288	174	182

Figure S74. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S75. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
5P GAIN MUTATED	13	44	58	26	14
5P GAIN WILD-TYPE	89	79	113	44	172

Figure S75. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.05

Table S76. Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
5P GAIN MUTATED	49	41	52	71
5P GAIN WILD-TYPE	133	140	135	126

Figure S76. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S77. Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
5P GAIN MUTATED	49	6	40	45	29	17	27
5P GAIN WILD-TYPE	148	58	76	102	30	54	66

Figure S77. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S78. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
5P GAIN MUTATED	18	86	101	31
5P GAIN WILD-TYPE	104	113	184	242

Figure S78. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S79. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
5P GAIN MUTATED	11	14	57	16	59	16	31	20	12
5P GAIN WILD-TYPE	77	47	91	68	62	22	80	39	157

Figure S79. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
5P GAIN MUTATED	42	59	133
5P GAIN WILD-TYPE	300	135	195

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S81. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
5P GAIN MUTATED	9	124	82	19
5P GAIN WILD-TYPE	67	223	151	189

Figure S81. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S82. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
5P GAIN MUTATED	17	9	17	51
5P GAIN WILD-TYPE	139	60	48	71

Figure S82. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S83. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
5P GAIN MUTATED	13	19	2	1	19	34	6
5P GAIN WILD-TYPE	78	64	47	19	27	43	40

Figure S83. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S84. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
5Q GAIN MUTATED	36	42	175
5Q GAIN WILD-TYPE	292	158	179

Figure S84. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S85. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
5Q GAIN MUTATED	12	45	68	28	13
5Q GAIN WILD-TYPE	90	78	103	42	173

Figure S85. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S86. Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
5Q GAIN MUTATED	50	6	38	56	30	18	30
5Q GAIN WILD-TYPE	147	58	78	91	29	53	63

Figure S86. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S87. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
5Q GAIN MUTATED	16	87	117	31
5Q GAIN WILD-TYPE	106	112	168	242

Figure S87. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S88. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
5Q GAIN MUTATED	11	11	64	16	61	16	37	25	10
5Q GAIN WILD-TYPE	77	50	84	68	60	22	74	34	159

Figure S88. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S89. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
5Q GAIN MUTATED	40	62	145
5Q GAIN WILD-TYPE	302	132	183

Figure S89. 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 = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
5Q GAIN MUTATED	9	125	94	19
5Q GAIN WILD-TYPE	67	222	139	189

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

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S91. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
5Q GAIN MUTATED	17	8	13	52
5Q GAIN WILD-TYPE	139	61	52	70

Figure S91. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S92. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
5Q GAIN MUTATED	13	15	2	0	18	36	6
5Q GAIN WILD-TYPE	78	68	47	20	28	41	40

Figure S92. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.066

Table S93. Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
6P GAIN MUTATED	7	1	9	4
6P GAIN WILD-TYPE	175	180	178	193

Figure S93. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.017

Table S94. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
6P GAIN MUTATED	1	3	3	8	2	0	2	2	1
6P GAIN WILD-TYPE	87	58	145	76	119	38	109	57	168

Figure S94. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0033

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
6P GAIN MUTATED	2	3	7	1
6P GAIN WILD-TYPE	154	66	58	121

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.038

Table S96. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
6P GAIN MUTATED	2	5	0	3	2	1	0
6P GAIN WILD-TYPE	89	78	49	17	44	76	46

Figure S96. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S97. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
7P GAIN MUTATED	202	20	147
7P GAIN WILD-TYPE	126	180	207

Figure S97. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S98. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
7P GAIN MUTATED	29	41	38	31	134
7P GAIN WILD-TYPE	73	82	133	39	52

Figure S98. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.016

Table S99. Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
7P GAIN MUTATED	62	73	75	100
7P GAIN WILD-TYPE	120	108	112	97

Figure S99. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0034

Table S100. Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
7P GAIN MUTATED	93	24	56	46	29	35	27
7P GAIN WILD-TYPE	104	40	60	101	30	36	66

Figure S100. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S101. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
7P GAIN MUTATED	37	88	71	171
7P GAIN WILD-TYPE	85	111	214	102

Figure S101. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S102. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
7P GAIN MUTATED	30	19	46	22	54	12	26	16	142
7P GAIN WILD-TYPE	58	42	102	62	67	26	85	43	27

Figure S102. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S103. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
7P GAIN MUTATED	192	67	107
7P GAIN WILD-TYPE	150	127	221

Figure S103. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S104. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
7P GAIN MUTATED	29	119	68	150
7P GAIN WILD-TYPE	47	228	165	58

Figure S104. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S105. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
7P GAIN MUTATED	109	23	25	40
7P GAIN WILD-TYPE	47	46	40	82

Figure S105. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S106. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
7P GAIN MUTATED	60	36	42	1	13	25	20
7P GAIN WILD-TYPE	31	47	7	19	33	52	26

Figure S106. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S107. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
7Q GAIN MUTATED	202	19	150
7Q GAIN WILD-TYPE	126	181	204

Figure S107. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S108. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
7Q GAIN MUTATED	29	43	40	32	134
7Q GAIN WILD-TYPE	73	80	131	38	52

Figure S108. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.022

Table S109. Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
7Q GAIN MUTATED	63	73	76	100
7Q GAIN WILD-TYPE	119	108	111	97

Figure S109. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0021

Table S110. Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
7Q GAIN MUTATED	96	24	56	43	29	34	30
7Q GAIN WILD-TYPE	101	40	60	104	30	37	63

Figure S110. 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 = 2.4e-05

Table S111. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
7Q GAIN MUTATED	37	89	72	171
7Q GAIN WILD-TYPE	85	110	213	102

Figure S111. 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 = 2.4e-05

Table S112. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
7Q GAIN MUTATED	30	19	46	22	55	14	26	15	142
7Q GAIN WILD-TYPE	58	42	102	62	66	24	85	44	27

Figure S112. 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 = 2.4e-05

Table S113. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
7Q GAIN MUTATED	192	70	106
7Q GAIN WILD-TYPE	150	124	222

Figure S113. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S114. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
7Q GAIN MUTATED	29	123	66	150
7Q GAIN WILD-TYPE	47	224	167	58

Figure S114. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S115. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
7Q GAIN MUTATED	109	23	25	39
7Q GAIN WILD-TYPE	47	46	40	83

Figure S115. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S116. Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
7Q GAIN MUTATED	60	36	42	1	13	24	20
7Q GAIN WILD-TYPE	31	47	7	19	33	53	26

Figure S116. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S117. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
8P GAIN MUTATED	33	0	36
8P GAIN WILD-TYPE	295	200	318

Figure S117. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S118. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
8P GAIN MUTATED	17	13	3	16	9
8P GAIN WILD-TYPE	85	110	168	54	177

Figure S118. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S119. Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
8P GAIN MUTATED	17	7	17	5	11	5	2
8P GAIN WILD-TYPE	180	57	99	142	48	66	91

Figure S119. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S120. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
8P GAIN MUTATED	19	28	5	17
8P GAIN WILD-TYPE	103	171	280	256

Figure S120. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S121. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
8P GAIN MUTATED	16	6	4	10	20	2	0	3	8
8P GAIN WILD-TYPE	72	55	144	74	101	36	111	56	161

Figure S121. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S122. Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
8P GAIN MUTATED	16	40	4	9
8P GAIN WILD-TYPE	60	307	229	199

Figure S122. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0015

Table S123. Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
8P GAIN MUTATED	10	14	11	6
8P GAIN WILD-TYPE	146	55	54	116

Figure S123. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0011

Table S124. Gene #15: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
8P GAIN MUTATED	6	13	2	0	3	4	13
8P GAIN WILD-TYPE	85	70	47	20	43	73	33

Figure S124. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S125. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
8Q GAIN MUTATED	37	2	64
8Q GAIN WILD-TYPE	291	198	290

Figure S125. 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 = 2.4e-05

Table S126. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
8Q GAIN MUTATED	20	24	5	21	11
8Q GAIN WILD-TYPE	82	99	166	49	175

Figure S126. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00605 (Fisher's exact test), Q value = 0.0097

Table S127. Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
8Q GAIN MUTATED	27	15	17	37
8Q GAIN WILD-TYPE	155	166	170	160

Figure S127. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00038

Table S128. Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
8Q GAIN MUTATED	23	7	26	10	16	7	7
8Q GAIN WILD-TYPE	174	57	90	137	43	64	86

Figure S128. 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 = 2.4e-05

Table S129. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
8Q GAIN MUTATED	22	51	8	21
8Q GAIN WILD-TYPE	100	148	277	252

Figure S129. 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 = 2.4e-05

Table S130. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
8Q GAIN MUTATED	17	10	7	12	40	4	0	4	8
8Q GAIN WILD-TYPE	71	51	141	72	81	34	111	55	161

Figure S130. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.038

Table S131. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
8Q GAIN MUTATED	35	34	33
8Q GAIN WILD-TYPE	307	160	295

Figure S131. 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 = 2.4e-05

Table S132. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
8Q GAIN MUTATED	17	67	8	10
8Q GAIN WILD-TYPE	59	280	225	198

Figure S132. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0025

Table S133. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
8Q GAIN MUTATED	11	16	14	13
8Q GAIN WILD-TYPE	145	53	51	109

Figure S133. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S134. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
8Q GAIN MUTATED	7	20	2	0	5	6	14
8Q GAIN WILD-TYPE	84	63	47	20	41	71	32

Figure S134. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S135. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
9P GAIN MUTATED	12	2	3	2	0
9P GAIN WILD-TYPE	90	121	168	68	186

Figure S135. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S136. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
9P GAIN MUTATED	14	2	9	1
9P GAIN WILD-TYPE	108	197	276	272

Figure S136. 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 = 2.4e-05

Table S137. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
9P GAIN MUTATED	12	4	3	1	0	2	4	0	0
9P GAIN WILD-TYPE	76	57	145	83	121	36	107	59	169

Figure S137. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S138. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
9P GAIN MUTATED	12	8	6	0
9P GAIN WILD-TYPE	64	339	227	208

Figure S138. 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 = 0.0012

Table S139. Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
9P GAIN MUTATED	1	8	4	3
9P GAIN WILD-TYPE	155	61	61	119

Figure S139. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S140. Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
9P GAIN MUTATED	0	3	0	0	2	3	8
9P GAIN WILD-TYPE	91	80	49	20	44	74	38

Figure S140. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.069

Table S141. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
9Q GAIN MUTATED	15	3	6
9Q GAIN WILD-TYPE	313	197	348

Figure S141. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S142. Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
9Q GAIN MUTATED	12	4	2	2	0
9Q GAIN WILD-TYPE	90	119	169	68	186

Figure S142. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S143. Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
9Q GAIN MUTATED	13	4	6	1
9Q GAIN WILD-TYPE	109	195	279	272

Figure S143. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S144. Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
9Q GAIN MUTATED	12	4	1	1	1	2	3	0	0
9Q GAIN WILD-TYPE	76	57	147	83	120	36	108	59	169

Figure S144. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S145. Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
9Q GAIN MUTATED	12	9	3	0
9Q GAIN WILD-TYPE	64	338	230	208

Figure S145. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00095

Table S146. Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
9Q GAIN MUTATED	1	8	3	2
9Q GAIN WILD-TYPE	155	61	62	120

Figure S146. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S147. Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
9Q GAIN MUTATED	0	2	0	0	2	2	8
9Q GAIN WILD-TYPE	91	81	49	20	44	75	38

Figure S147. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.028

Table S148. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
10P GAIN MUTATED	11	1	16
10P GAIN WILD-TYPE	317	199	338

Figure S148. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.0054

Table S149. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
10P GAIN MUTATED	6	13	3	6
10P GAIN WILD-TYPE	116	186	282	267

Figure S149. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00574 (Fisher's exact test), Q value = 0.0093

Table S150. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
10P GAIN MUTATED	4	5	2	2	9	2	0	1	3
10P GAIN WILD-TYPE	84	56	146	82	112	36	111	58	166

Figure S150. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.013

Table S151. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
10P GAIN MUTATED	3	19	2	4
10P GAIN WILD-TYPE	73	328	231	204

Figure S151. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.057

Table S152. Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
10Q GAIN MUTATED	0	0	1	2
10Q GAIN WILD-TYPE	31	25	12	15

Figure S152. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0021

Table S153. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
11P GAIN MUTATED	26	3	29
11P GAIN WILD-TYPE	302	197	325

Figure S153. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S154. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
11P GAIN MUTATED	19	6	7	7	4
11P GAIN WILD-TYPE	83	117	164	63	182

Figure S154. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S155. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
11P GAIN MUTATED	22	15	13	8
11P GAIN WILD-TYPE	100	184	272	265

Figure S155. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S156. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
11P GAIN MUTATED	19	6	7	5	11	3	4	2	1
11P GAIN WILD-TYPE	69	55	141	79	110	35	107	57	168

Figure S156. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S157. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
11P GAIN MUTATED	18	24	9	7
11P GAIN WILD-TYPE	58	323	224	201

Figure S157. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S158. Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
11P GAIN MUTATED	5	14	4	4
11P GAIN WILD-TYPE	151	55	61	118

Figure S158. 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 = 2.4e-05

Table S159. Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
11P GAIN MUTATED	3	6	0	0	2	2	14
11P GAIN WILD-TYPE	88	77	49	20	44	75	32

Figure S159. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0041

Table S160. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
11Q GAIN MUTATED	24	3	28
11Q GAIN WILD-TYPE	304	197	326

Figure S160. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S161. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
11Q GAIN MUTATED	20	2	7	6	5
11Q GAIN WILD-TYPE	82	121	164	64	181

Figure S161. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S162. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
11Q GAIN MUTATED	22	12	14	7
11Q GAIN WILD-TYPE	100	187	271	266

Figure S162. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S163. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
11Q GAIN MUTATED	20	4	8	5	8	3	4	2	1
11Q GAIN WILD-TYPE	68	57	140	79	113	35	107	57	168

Figure S163. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S164. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
11Q GAIN MUTATED	19	21	10	5
11Q GAIN WILD-TYPE	57	326	223	203

Figure S164. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S165. Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
11Q GAIN MUTATED	4	15	3	4
11Q GAIN WILD-TYPE	152	54	62	118

Figure S165. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S166. Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
11Q GAIN MUTATED	3	5	0	0	1	2	15
11Q GAIN WILD-TYPE	88	78	49	20	45	75	31

Figure S166. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.046

Table S167. Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
12P GAIN MUTATED	3	10	2	6
12P GAIN WILD-TYPE	28	15	11	11

Figure S167. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S168. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
12P GAIN MUTATED	131	10	111
12P GAIN WILD-TYPE	197	190	243

Figure S168. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S169. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
12P GAIN MUTATED	25	41	25	30	80
12P GAIN WILD-TYPE	77	82	146	40	106

Figure S169. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.043

Table S170. Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
12P GAIN MUTATED	53	38	49	68
12P GAIN WILD-TYPE	129	143	138	129

Figure S170. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S171. Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
12P GAIN MUTATED	48	15	45	24	29	24	23
12P GAIN WILD-TYPE	149	49	71	123	30	47	70

Figure S171. 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 = 2.4e-05

Table S172. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
12P GAIN MUTATED	29	75	36	111
12P GAIN WILD-TYPE	93	124	249	162

Figure S172. 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 = 2.4e-05

Table S173. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
12P GAIN MUTATED	24	20	22	19	54	11	10	9	82
12P GAIN WILD-TYPE	64	41	126	65	67	27	101	50	87

Figure S173. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S174. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
12P GAIN MUTATED	129	49	72
12P GAIN WILD-TYPE	213	145	256

Figure S174. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S175. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
12P GAIN MUTATED	22	110	30	88
12P GAIN WILD-TYPE	54	237	203	120

Figure S175. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00048

Table S176. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
12P GAIN MUTATED	67	19	20	23
12P GAIN WILD-TYPE	89	50	45	99

Figure S176. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S177. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
12P GAIN MUTATED	44	33	15	0	9	12	16
12P GAIN WILD-TYPE	47	50	34	20	37	65	30

Figure S177. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.045

Table S178. Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
12Q GAIN MUTATED	3	10	2	6
12Q GAIN WILD-TYPE	28	15	11	11

Figure S178. 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 = 2.4e-05

Table S179. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
12Q GAIN MUTATED	134	10	112
12Q GAIN WILD-TYPE	194	190	242

Figure S179. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S180. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
12Q GAIN MUTATED	27	42	25	30	80
12Q GAIN WILD-TYPE	75	81	146	40	106

Figure S180. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.018

Table S181. Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
12Q GAIN MUTATED	54	38	49	71
12Q GAIN WILD-TYPE	128	143	138	126

Figure S181. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S182. Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
12Q GAIN MUTATED	48	15	47	24	31	24	23
12Q GAIN WILD-TYPE	149	49	69	123	28	47	70

Figure S182. 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 = 2.4e-05

Table S183. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
12Q GAIN MUTATED	31	77	36	111
12Q GAIN WILD-TYPE	91	122	249	162

Figure S183. 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 = 2.4e-05

Table S184. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
12Q GAIN MUTATED	26	21	22	19	55	11	10	9	82
12Q GAIN WILD-TYPE	62	40	126	65	66	27	101	50	87

Figure S184. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S185. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
12Q GAIN MUTATED	131	50	73
12Q GAIN WILD-TYPE	211	144	255

Figure S185. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S186. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
12Q GAIN MUTATED	24	112	30	88
12Q GAIN WILD-TYPE	52	235	203	120

Figure S186. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00059

Table S187. Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
12Q GAIN MUTATED	67	21	21	23
12Q GAIN WILD-TYPE	89	48	44	99

Figure S187. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S188. Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
12Q GAIN MUTATED	44	34	15	0	9	12	18
12Q GAIN WILD-TYPE	47	49	34	20	37	65	28

Figure S188. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.0055

Table S189. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
13Q GAIN MUTATED	29	4	19
13Q GAIN WILD-TYPE	299	196	335

Figure S189. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.05

Table S190. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
13Q GAIN MUTATED	6	9	11	26
13Q GAIN WILD-TYPE	116	190	274	247

Figure S190. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.027

Table S191. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
13Q GAIN MUTATED	3	3	11	6	7	0	3	0	19
13Q GAIN WILD-TYPE	85	58	137	78	114	38	108	59	150

Figure S191. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.054

Table S192. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
13Q GAIN MUTATED	29	9	13
13Q GAIN WILD-TYPE	313	185	315

Figure S192. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.023

Table S193. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
13Q GAIN MUTATED	2	18	9	22
13Q GAIN WILD-TYPE	74	329	224	186

Figure S193. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.001

Table S194. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
14Q GAIN MUTATED	25	2	12
14Q GAIN WILD-TYPE	303	198	342

Figure S194. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S195. Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
14Q GAIN MUTATED	25	7	0	1	0
14Q GAIN WILD-TYPE	77	116	171	69	186

Figure S195. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.0044

Table S196. Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
14Q GAIN MUTATED	10	5	12	2	5	1	1
14Q GAIN WILD-TYPE	187	59	104	145	54	70	92

Figure S196. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S197. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
14Q GAIN MUTATED	27	8	3	1
14Q GAIN WILD-TYPE	95	191	282	272

Figure S197. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S198. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
14Q GAIN MUTATED	25	5	2	1	4	0	1	1	0
14Q GAIN WILD-TYPE	63	56	146	83	117	38	110	58	169

Figure S198. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0017

Table S199. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
14Q GAIN MUTATED	26	3	9
14Q GAIN WILD-TYPE	316	191	319

Figure S199. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S200. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
14Q GAIN MUTATED	24	12	2	0
14Q GAIN WILD-TYPE	52	335	231	208

Figure S200. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S201. Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
14Q GAIN MUTATED	0	18	3	0
14Q GAIN WILD-TYPE	156	51	62	122

Figure S201. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S202. Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
14Q GAIN MUTATED	0	3	0	0	1	0	17
14Q GAIN WILD-TYPE	91	80	49	20	45	77	29

Figure S202. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00084

Table S203. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
15Q GAIN MUTATED	27	2	23
15Q GAIN WILD-TYPE	301	198	331

Figure S203. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S204. Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
15Q GAIN MUTATED	23	1	7	5	3
15Q GAIN WILD-TYPE	79	122	164	65	183

Figure S204. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.046

Table S205. Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
15Q GAIN MUTATED	12	4	12	9	8	1	2
15Q GAIN WILD-TYPE	185	60	104	138	51	70	91

Figure S205. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S206. Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
15Q GAIN MUTATED	25	10	12	4
15Q GAIN WILD-TYPE	97	189	273	269

Figure S206. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S207. Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
15Q GAIN MUTATED	24	2	8	3	4	4	2	3	1
15Q GAIN WILD-TYPE	64	59	140	81	117	34	109	56	168

Figure S207. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S208. Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
15Q GAIN MUTATED	24	16	9	2
15Q GAIN WILD-TYPE	52	331	224	206

Figure S208. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S209. Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
15Q GAIN MUTATED	0	17	1	5
15Q GAIN WILD-TYPE	156	52	64	117

Figure S209. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S210. Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
15Q GAIN MUTATED	0	1	0	0	0	5	17
15Q GAIN WILD-TYPE	91	82	49	20	46	72	29

Figure S210. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S211. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
16P GAIN MUTATED	172	11	98
16P GAIN WILD-TYPE	156	189	256

Figure S211. 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 = 2.4e-05

Table S212. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
16P GAIN MUTATED	27	28	26	27	119
16P GAIN WILD-TYPE	75	95	145	43	67

Figure S212. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.0084

Table S213. Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
16P GAIN MUTATED	42	53	75	60
16P GAIN WILD-TYPE	140	128	112	137

Figure S213. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00093

Table S214. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
16P GAIN MUTATED	60	33	32	36	22	28	19
16P GAIN WILD-TYPE	137	31	84	111	37	43	74

Figure S214. 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 = 2.4e-05

Table S215. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
16P GAIN MUTATED	33	49	45	154
16P GAIN WILD-TYPE	89	150	240	119

Figure S215. 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 = 2.4e-05

Table S216. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
16P GAIN MUTATED	27	11	24	38	35	6	17	11	112
16P GAIN WILD-TYPE	61	50	124	46	86	32	94	48	57

Figure S216. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S217. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
16P GAIN MUTATED	178	35	67
16P GAIN WILD-TYPE	164	159	261

Figure S217. 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 = 2.4e-05

Table S218. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
16P GAIN MUTATED	24	89	36	131
16P GAIN WILD-TYPE	52	258	197	77

Figure S218. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S219. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
16P GAIN MUTATED	96	20	20	25
16P GAIN WILD-TYPE	60	49	45	97

Figure S219. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S220. Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
16P GAIN MUTATED	64	29	26	0	9	15	18
16P GAIN WILD-TYPE	27	54	23	20	37	62	28

Figure S220. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S221. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
16Q GAIN MUTATED	170	11	87
16Q GAIN WILD-TYPE	158	189	267

Figure S221. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S222. Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
16Q GAIN MUTATED	27	27	23	22	119
16Q GAIN WILD-TYPE	75	96	148	48	67

Figure S222. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0048

Table S223. Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
16Q GAIN MUTATED	39	50	73	58
16Q GAIN WILD-TYPE	143	131	114	139

Figure S223. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S224. Gene #29: '16q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
16Q GAIN MUTATED	57	32	31	33	22	27	18
16Q GAIN WILD-TYPE	140	32	85	114	37	44	75

Figure S224. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S225. Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
16Q GAIN MUTATED	31	48	41	148
16Q GAIN WILD-TYPE	91	151	244	125

Figure S225. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S226. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
16Q GAIN MUTATED	26	11	19	33	34	6	17	11	111
16Q GAIN WILD-TYPE	62	50	129	51	87	32	94	48	58

Figure S226. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S227. Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
16Q GAIN MUTATED	173	34	60
16Q GAIN WILD-TYPE	169	160	268

Figure S227. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S228. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
16Q GAIN MUTATED	24	78	34	131
16Q GAIN WILD-TYPE	52	269	199	77

Figure S228. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S229. Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
16Q GAIN MUTATED	94	20	17	22
16Q GAIN WILD-TYPE	62	49	48	100

Figure S229. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S230. Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
16Q GAIN MUTATED	64	25	25	0	8	13	18
16Q GAIN WILD-TYPE	27	58	24	20	38	64	28

Figure S230. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S231. Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
17P GAIN MUTATED	1	0	2	11
17P GAIN WILD-TYPE	30	25	11	6

Figure S231. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S232. Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S232. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S233. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
17P GAIN MUTATED	172	1	23
17P GAIN WILD-TYPE	156	199	331

Figure S233. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S234. Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
17P GAIN MUTATED	5	18	7	8	140
17P GAIN WILD-TYPE	97	105	164	62	46

Figure S234. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.045

Table S235. Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
17P GAIN MUTATED	25	44	44	35
17P GAIN WILD-TYPE	157	137	143	162

Figure S235. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0013

Table S236. Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
17P GAIN MUTATED	50	16	21	23	6	23	9
17P GAIN WILD-TYPE	147	48	95	124	53	48	84

Figure S236. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S237. Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
17P GAIN MUTATED	6	12	9	169
17P GAIN WILD-TYPE	116	187	276	104

Figure S237. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S238. Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
17P GAIN MUTATED	1	12	6	19	6	3	1	1	147
17P GAIN WILD-TYPE	87	49	142	65	115	35	110	58	22

Figure S238. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S239. Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
17P GAIN MUTATED	168	15	12
17P GAIN WILD-TYPE	174	179	316

Figure S239. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S240. Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
17P GAIN MUTATED	0	36	7	152
17P GAIN WILD-TYPE	76	311	226	56

Figure S240. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S241. Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
17P GAIN MUTATED	109	5	14	3
17P GAIN WILD-TYPE	47	64	51	119

Figure S241. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S242. Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
17P GAIN MUTATED	62	20	44	2	2	1	0
17P GAIN WILD-TYPE	29	63	5	18	44	76	46

Figure S242. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S243. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
17Q GAIN MUTATED	1	1	2	12
17Q GAIN WILD-TYPE	30	24	11	5

Figure S243. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S244. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17Q GAIN MUTATED	1	1	13	0	1
17Q GAIN WILD-TYPE	19	23	5	13	10

Figure S244. 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 = 2.4e-05

Table S245. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
17Q GAIN MUTATED	184	3	35
17Q GAIN WILD-TYPE	144	197	319

Figure S245. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S246. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
17Q GAIN MUTATED	7	24	8	16	144
17Q GAIN WILD-TYPE	95	99	163	54	42

Figure S246. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.0056

Table S247. Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
17Q GAIN MUTATED	51	20	24	25	7	26	16
17Q GAIN WILD-TYPE	146	44	92	122	52	45	77

Figure S247. 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 = 2.4e-05

Table S248. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
17Q GAIN MUTATED	8	18	10	186
17Q GAIN WILD-TYPE	114	181	275	87

Figure S248. 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 = 2.4e-05

Table S249. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
17Q GAIN MUTATED	1	16	7	32	10	4	1	2	149
17Q GAIN WILD-TYPE	87	45	141	52	111	34	110	57	20

Figure S249. 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 = 2.4e-05

Table S250. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
17Q GAIN MUTATED	180	28	13
17Q GAIN WILD-TYPE	162	166	315

Figure S250. 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 = 2.4e-05

Table S251. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
17Q GAIN MUTATED	0	53	8	160
17Q GAIN WILD-TYPE	76	294	225	48

Figure S251. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S252. Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
17Q GAIN MUTATED	117	5	24	3
17Q GAIN WILD-TYPE	39	64	41	119

Figure S252. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S253. Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
17Q GAIN MUTATED	66	32	45	2	3	1	0
17Q GAIN WILD-TYPE	25	51	4	18	43	76	46

Figure S253. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S254. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
18P GAIN MUTATED	19	0	11	2	8
18P GAIN WILD-TYPE	83	123	160	68	178

Figure S254. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S255. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
18P GAIN MUTATED	21	8	14	11
18P GAIN WILD-TYPE	101	191	271	262

Figure S255. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00036

Table S256. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
18P GAIN MUTATED	18	4	6	2	3	1	8	4	8
18P GAIN WILD-TYPE	70	57	142	82	118	37	103	55	161

Figure S256. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.035

Table S257. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
18P GAIN MUTATED	30	6	17
18P GAIN WILD-TYPE	312	188	311

Figure S257. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S258. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
18P GAIN MUTATED	17	16	12	8
18P GAIN WILD-TYPE	59	331	221	200

Figure S258. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0017

Table S259. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
18P GAIN MUTATED	8	15	3	8
18P GAIN WILD-TYPE	148	54	62	114

Figure S259. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0018

Table S260. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
18P GAIN MUTATED	5	4	3	1	1	7	13
18P GAIN WILD-TYPE	86	79	46	19	45	70	33

Figure S260. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S261. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
18Q GAIN MUTATED	18	0	11	2	7
18Q GAIN WILD-TYPE	84	123	160	68	179

Figure S261. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S262. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
18Q GAIN MUTATED	20	8	14	8
18Q GAIN WILD-TYPE	102	191	271	265

Figure S262. 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 = 2.4e-05

Table S263. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
18Q GAIN MUTATED	18	3	5	0	4	1	8	4	7
18Q GAIN WILD-TYPE	70	58	143	84	117	37	103	55	162

Figure S263. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.065

Table S264. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
18Q GAIN MUTATED	26	5	18
18Q GAIN WILD-TYPE	316	189	310

Figure S264. 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 = 2.4e-05

Table S265. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
18Q GAIN MUTATED	17	13	12	7
18Q GAIN WILD-TYPE	59	334	221	201

Figure S265. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00059

Table S266. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
18Q GAIN MUTATED	7	14	1	8
18Q GAIN WILD-TYPE	149	55	64	114

Figure S266. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S267. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
18Q GAIN MUTATED	5	1	2	1	1	7	13
18Q GAIN WILD-TYPE	86	82	47	19	45	70	33

Figure S267. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S268. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
19P GAIN MUTATED	25	3	46
19P GAIN WILD-TYPE	303	197	308

Figure S268. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S269. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
19P GAIN MUTATED	24	8	11	13	2
19P GAIN WILD-TYPE	78	115	160	57	184

Figure S269. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0038

Table S270. Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
19P GAIN MUTATED	18	2	17	9	13	3	7
19P GAIN WILD-TYPE	179	62	99	138	46	68	86

Figure S270. 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 = 2.4e-05

Table S271. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
19P GAIN MUTATED	27	28	17	2
19P GAIN WILD-TYPE	95	171	268	271

Figure S271. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S272. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
19P GAIN MUTATED	25	6	10	1	21	3	5	3	0
19P GAIN WILD-TYPE	63	55	138	83	100	35	106	56	169

Figure S272. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S273. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
19P GAIN MUTATED	23	34	15	1
19P GAIN WILD-TYPE	53	313	218	207

Figure S273. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S274. Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
19P GAIN MUTATED	1	16	2	11
19P GAIN WILD-TYPE	155	53	63	111

Figure S274. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S275. Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
19P GAIN MUTATED	1	3	0	0	3	7	16
19P GAIN WILD-TYPE	90	80	49	20	43	70	30

Figure S275. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S276. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
19Q GAIN MUTATED	24	3	51
19Q GAIN WILD-TYPE	304	197	303

Figure S276. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S277. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
19Q GAIN MUTATED	23	7	11	16	2
19Q GAIN WILD-TYPE	79	116	160	54	184

Figure S277. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S278. Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
19Q GAIN MUTATED	19	2	19	9	14	3	7
19Q GAIN WILD-TYPE	178	62	97	138	45	68	86

Figure S278. 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 = 2.4e-05

Table S279. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
19Q GAIN MUTATED	26	31	18	2
19Q GAIN WILD-TYPE	96	168	267	271

Figure S279. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S280. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
19Q GAIN MUTATED	24	5	11	1	25	3	5	3	0
19Q GAIN WILD-TYPE	64	56	137	83	96	35	106	56	169

Figure S280. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S281. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
19Q GAIN MUTATED	22	37	16	1
19Q GAIN WILD-TYPE	54	310	217	207

Figure S281. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S282. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
19Q GAIN MUTATED	1	15	2	12
19Q GAIN WILD-TYPE	155	54	63	110

Figure S282. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S283. Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
19Q GAIN MUTATED	1	3	0	0	3	8	15
19Q GAIN WILD-TYPE	90	80	49	20	43	69	31

Figure S283. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S284. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
20P GAIN MUTATED	119	7	107
20P GAIN WILD-TYPE	209	193	247

Figure S284. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S285. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
20P GAIN MUTATED	26	38	15	28	71
20P GAIN WILD-TYPE	76	85	156	42	115

Figure S285. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.028

Table S286. Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
20P GAIN MUTATED	45	41	39	67
20P GAIN WILD-TYPE	137	140	148	130

Figure S286. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S287. Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
20P GAIN MUTATED	52	9	47	23	27	16	18
20P GAIN WILD-TYPE	145	55	69	124	32	55	75

Figure S287. 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 = 2.4e-05

Table S288. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
20P GAIN MUTATED	31	83	26	93
20P GAIN WILD-TYPE	91	116	259	180

Figure S288. 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 = 2.4e-05

Table S289. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
20P GAIN MUTATED	26	18	19	14	62	4	8	7	75
20P GAIN WILD-TYPE	62	43	129	70	59	34	103	52	94

Figure S289. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00019

Table S290. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
20P GAIN MUTATED	118	50	64
20P GAIN WILD-TYPE	224	144	264

Figure S290. 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 = 2.4e-05

Table S291. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
20P GAIN MUTATED	24	99	28	81
20P GAIN WILD-TYPE	52	248	205	127

Figure S291. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.011

Table S292. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
20P GAIN MUTATED	57	20	21	22
20P GAIN WILD-TYPE	99	49	44	100

Figure S292. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00025

Table S293. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
20P GAIN MUTATED	38	28	14	1	14	9	16
20P GAIN WILD-TYPE	53	55	35	19	32	68	30

Figure S293. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.052

Table S294. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
20Q GAIN MUTATED	3	8	5	7
20Q GAIN WILD-TYPE	28	17	8	10

Figure S294. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.071

Table S295. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
20Q GAIN MUTATED	2	8	8	1	4
20Q GAIN WILD-TYPE	18	16	10	12	7

Figure S295. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S296. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
20Q GAIN MUTATED	119	8	110
20Q GAIN WILD-TYPE	209	192	244

Figure S296. 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 = 2.4e-05

Table S297. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
20Q GAIN MUTATED	27	37	15	29	71
20Q GAIN WILD-TYPE	75	86	156	41	115

Figure S297. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.015

Table S298. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
20Q GAIN MUTATED	46	40	40	69
20Q GAIN WILD-TYPE	136	141	147	128

Figure S298. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S299. Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
20Q GAIN MUTATED	52	10	47	22	29	16	19
20Q GAIN WILD-TYPE	145	54	69	125	30	55	74

Figure S299. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S300. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
20Q GAIN MUTATED	32	86	26	93
20Q GAIN WILD-TYPE	90	113	259	180

Figure S300. 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 = 2.4e-05

Table S301. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
20Q GAIN MUTATED	26	19	19	15	65	4	8	7	74
20Q GAIN WILD-TYPE	62	42	129	69	56	34	103	52	95

Figure S301. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00021

Table S302. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
20Q GAIN MUTATED	120	51	65
20Q GAIN WILD-TYPE	222	143	263

Figure S302. 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 = 2.4e-05

Table S303. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
20Q GAIN MUTATED	24	103	28	81
20Q GAIN WILD-TYPE	52	244	205	127

Figure S303. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.013

Table S304. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
20Q GAIN MUTATED	57	20	23	23
20Q GAIN WILD-TYPE	99	49	42	99

Figure S304. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S305. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
20Q GAIN MUTATED	38	30	14	1	14	10	16
20Q GAIN WILD-TYPE	53	53	35	19	32	67	30

Figure S305. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S306. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
21Q GAIN MUTATED	21	1	50
21Q GAIN WILD-TYPE	307	199	304

Figure S306. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.071

Table S307. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
21Q GAIN MUTATED	5	11	10	12	13
21Q GAIN WILD-TYPE	97	112	161	58	173

Figure S307. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.031

Table S308. Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
21Q GAIN MUTATED	12	2	10	13	13	6	7
21Q GAIN WILD-TYPE	185	62	106	134	46	65	86

Figure S308. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S309. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
21Q GAIN MUTATED	8	33	14	17
21Q GAIN WILD-TYPE	114	166	271	256

Figure S309. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0023

Table S310. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
21Q GAIN MUTATED	5	5	8	2	24	4	6	5	13
21Q GAIN WILD-TYPE	83	56	140	82	97	34	105	54	156

Figure S310. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

Table S311. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
22Q GAIN MUTATED	28	3	33
22Q GAIN WILD-TYPE	300	197	321

Figure S311. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S312. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
22Q GAIN MUTATED	21	6	10	7	3
22Q GAIN WILD-TYPE	81	117	161	63	183

Figure S312. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S313. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
22Q GAIN MUTATED	24	20	16	4
22Q GAIN WILD-TYPE	98	179	269	269

Figure S313. 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 = 2.4e-05

Table S314. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
22Q GAIN MUTATED	23	3	10	1	16	3	4	1	3
22Q GAIN WILD-TYPE	65	58	138	83	105	35	107	58	166

Figure S314. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S315. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
22Q GAIN MUTATED	22	22	16	3
22Q GAIN WILD-TYPE	54	325	217	205

Figure S315. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S316. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
22Q GAIN MUTATED	3	16	3	3
22Q GAIN WILD-TYPE	153	53	62	119

Figure S316. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S317. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
22Q GAIN MUTATED	2	1	1	0	3	2	16
22Q GAIN WILD-TYPE	89	82	48	20	43	75	30

Figure S317. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.017

Table S318. Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
XP GAIN MUTATED	2	2	1	7
XP GAIN WILD-TYPE	29	23	12	10

Figure S318. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0089 (Fisher's exact test), Q value = 0.014

Table S319. Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
XP GAIN MUTATED	0	2	7	2	1
XP GAIN WILD-TYPE	20	22	11	11	10

Figure S319. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S320. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
XP GAIN MUTATED	98	5	26
XP GAIN WILD-TYPE	230	195	328

Figure S320. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S321. Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
XP GAIN MUTATED	11	10	4	6	74
XP GAIN WILD-TYPE	91	113	167	64	112

Figure S321. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0038

Table S322. Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
XP GAIN MUTATED	32	10	21	11	5	16	5
XP GAIN WILD-TYPE	165	54	95	136	54	55	88

Figure S322. 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 = 2.4e-05

Table S323. Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
XP GAIN MUTATED	13	20	9	87
XP GAIN WILD-TYPE	109	179	276	186

Figure S323. 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 = 2.4e-05

Table S324. Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
XP GAIN MUTATED	9	5	4	10	17	2	4	0	78
XP GAIN WILD-TYPE	79	56	144	74	104	36	107	59	91

Figure S324. 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 = 2.4e-05

Table S325. Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
XP GAIN MUTATED	97	13	19
XP GAIN WILD-TYPE	245	181	309

Figure S325. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S326. Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
XP GAIN MUTATED	8	31	9	81
XP GAIN WILD-TYPE	68	316	224	127

Figure S326. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S327. Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
XP GAIN MUTATED	56	9	3	7
XP GAIN WILD-TYPE	100	60	62	115

Figure S327. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S328. Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
XP GAIN MUTATED	35	11	17	1	3	2	6
XP GAIN WILD-TYPE	56	72	32	19	43	75	40

Figure S328. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00046

Table S329. Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
XQ GAIN MUTATED	3	0	1	8
XQ GAIN WILD-TYPE	28	25	12	9

Figure S329. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0011

Table S330. Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
XQ GAIN MUTATED	1	0	8	2	1
XQ GAIN WILD-TYPE	19	24	10	11	10

Figure S330. 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 = 2.4e-05

Table S331. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
XQ GAIN MUTATED	97	7	26
XQ GAIN WILD-TYPE	231	193	328

Figure S331. 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 = 2.4e-05

Table S332. Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
XQ GAIN MUTATED	11	11	5	6	74
XQ GAIN WILD-TYPE	91	112	166	64	112

Figure S332. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00438 (Fisher's exact test), Q value = 0.0072

Table S333. Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
XQ GAIN MUTATED	33	10	19	13	4	16	5
XQ GAIN WILD-TYPE	164	54	97	134	55	55	88

Figure S333. 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 = 2.4e-05

Table S334. Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
XQ GAIN MUTATED	13	17	12	88
XQ GAIN WILD-TYPE	109	182	273	185

Figure S334. 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 = 2.4e-05

Table S335. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
XQ GAIN MUTATED	9	5	5	10	14	3	5	1	78
XQ GAIN WILD-TYPE	79	56	143	74	107	35	106	58	91

Figure S335. 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 = 2.4e-05

Table S336. Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
XQ GAIN MUTATED	99	12	19
XQ GAIN WILD-TYPE	243	182	309

Figure S336. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S337. Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
XQ GAIN MUTATED	8	28	11	83
XQ GAIN WILD-TYPE	68	319	222	125

Figure S337. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S338. Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
XQ GAIN MUTATED	57	9	3	7
XQ GAIN WILD-TYPE	99	60	62	115

Figure S338. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S339. Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
XQ GAIN MUTATED	35	13	17	1	2	2	6
XQ GAIN WILD-TYPE	56	70	32	19	44	75	40

Figure S339. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.0053

Table S340. Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
1P LOSS MUTATED	2	3	7	2
1P LOSS WILD-TYPE	29	22	6	15

Figure S340. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.02

Table S341. Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
1P LOSS MUTATED	1	3	3	1	6
1P LOSS WILD-TYPE	19	21	15	12	5

Figure S341. 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 = 2.4e-05

Table S342. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
1P LOSS MUTATED	87	13	45
1P LOSS WILD-TYPE	241	187	309

Figure S342. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S343. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
1P LOSS MUTATED	61	12	14	14	14
1P LOSS WILD-TYPE	41	111	157	56	172

Figure S343. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S344. Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
1P LOSS MUTATED	34	18	36	15	10	6	10
1P LOSS WILD-TYPE	163	46	80	132	49	65	83

Figure S344. 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 = 2.4e-05

Table S345. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
1P LOSS MUTATED	70	20	24	31
1P LOSS WILD-TYPE	52	179	261	242

Figure S345. 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 = 2.4e-05

Table S346. Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
1P LOSS MUTATED	69	14	14	15	11	2	6	6	8
1P LOSS WILD-TYPE	19	47	134	69	110	36	105	53	161

Figure S346. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S347. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
1P LOSS MUTATED	92	20	33
1P LOSS WILD-TYPE	250	174	295

Figure S347. 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 = 2.4e-05

Table S348. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
1P LOSS MUTATED	67	37	20	21
1P LOSS WILD-TYPE	9	310	213	187

Figure S348. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S349. Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
1P LOSS MUTATED	14	42	8	8
1P LOSS WILD-TYPE	142	27	57	114

Figure S349. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S350. Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
1P LOSS MUTATED	11	9	1	2	5	5	39
1P LOSS WILD-TYPE	80	74	48	18	41	72	7

Figure S350. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MRNA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.028

Table S351. Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
1Q LOSS MUTATED	2	1	5	2
1Q LOSS WILD-TYPE	29	24	8	15

Figure S351. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.021

Table S352. Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
1Q LOSS MUTATED	1	1	2	1	5
1Q LOSS WILD-TYPE	19	23	16	12	6

Figure S352. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S353. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
1Q LOSS MUTATED	80	7	23
1Q LOSS WILD-TYPE	248	193	331

Figure S353. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S354. Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
1Q LOSS MUTATED	56	9	10	5	11
1Q LOSS WILD-TYPE	46	114	161	65	175

Figure S354. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S355. Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
1Q LOSS MUTATED	28	13	33	10	7	3	4
1Q LOSS WILD-TYPE	169	51	83	137	52	68	89

Figure S355. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S356. Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
1Q LOSS MUTATED	65	13	14	18
1Q LOSS WILD-TYPE	57	186	271	255

Figure S356. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S357. Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
1Q LOSS MUTATED	65	10	6	5	6	2	5	3	8
1Q LOSS WILD-TYPE	23	51	142	79	115	36	106	56	161

Figure S357. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S358. Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
1Q LOSS MUTATED	77	14	19
1Q LOSS WILD-TYPE	265	180	309

Figure S358. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S359. Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
1Q LOSS MUTATED	64	17	12	17
1Q LOSS WILD-TYPE	12	330	221	191

Figure S359. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S360. Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
1Q LOSS MUTATED	9	38	5	7
1Q LOSS WILD-TYPE	147	31	60	115

Figure S360. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S361. Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
1Q LOSS MUTATED	7	4	1	0	5	4	38
1Q LOSS WILD-TYPE	84	79	48	20	41	73	8

Figure S361. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S362. Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
2P LOSS MUTATED	0	1	6	0
2P LOSS WILD-TYPE	31	24	7	17

Figure S362. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00079

Table S363. Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
2P LOSS MUTATED	0	1	1	0	5
2P LOSS WILD-TYPE	20	23	17	13	6

Figure S363. 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 = 2.4e-05

Table S364. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
2P LOSS MUTATED	57	4	4
2P LOSS WILD-TYPE	271	196	350

Figure S364. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S365. Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
2P LOSS MUTATED	52	1	0	4	0
2P LOSS WILD-TYPE	50	122	171	66	186

Figure S365. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S366. Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
2P LOSS MUTATED	15	13	21	3	3	1	1
2P LOSS WILD-TYPE	182	51	95	144	56	70	92

Figure S366. 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 = 2.4e-05

Table S367. Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
2P LOSS MUTATED	60	2	0	3
2P LOSS WILD-TYPE	62	197	285	270

Figure S367. 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 = 2.4e-05

Table S368. Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
2P LOSS MUTATED	58	1	0	4	2	0	0	0	0
2P LOSS WILD-TYPE	30	60	148	80	119	38	111	59	169

Figure S368. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S369. Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
2P LOSS MUTATED	60	2	3
2P LOSS WILD-TYPE	282	192	325

Figure S369. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S370. Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
2P LOSS MUTATED	57	6	0	2
2P LOSS WILD-TYPE	19	341	233	206

Figure S370. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S371. Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
2P LOSS MUTATED	1	36	0	1
2P LOSS WILD-TYPE	155	33	65	121

Figure S371. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S372. Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
2P LOSS MUTATED	1	1	0	0	0	1	35
2P LOSS WILD-TYPE	90	82	49	20	46	76	11

Figure S372. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00036

Table S373. Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
2Q LOSS MUTATED	0	1	5	0
2Q LOSS WILD-TYPE	31	24	8	17

Figure S373. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S374. Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
2Q LOSS MUTATED	0	1	0	0	5
2Q LOSS WILD-TYPE	20	23	18	13	6

Figure S374. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S375. Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
2Q LOSS MUTATED	55	4	4
2Q LOSS WILD-TYPE	273	196	350

Figure S375. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S376. Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
2Q LOSS MUTATED	52	2	0	2	0
2Q LOSS WILD-TYPE	50	121	171	68	186

Figure S376. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S377. Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
2Q LOSS MUTATED	15	12	21	3	3	1	1
2Q LOSS WILD-TYPE	182	52	95	144	56	70	92

Figure S377. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S378. Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
2Q LOSS MUTATED	59	3	0	1
2Q LOSS WILD-TYPE	63	196	285	272

Figure S378. 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 = 2.4e-05

Table S379. Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
2Q LOSS MUTATED	58	2	0	1	2	0	0	0	0
2Q LOSS WILD-TYPE	30	59	148	83	119	38	111	59	169

Figure S379. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S380. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
2Q LOSS MUTATED	58	1	4
2Q LOSS WILD-TYPE	284	193	324

Figure S380. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S381. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
2Q LOSS MUTATED	57	5	0	1
2Q LOSS WILD-TYPE	19	342	233	207

Figure S381. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S382. Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
2Q LOSS MUTATED	1	36	0	1
2Q LOSS WILD-TYPE	155	33	65	121

Figure S382. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S383. Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
2Q LOSS MUTATED	1	1	0	0	0	1	35
2Q LOSS WILD-TYPE	90	82	49	20	46	76	11

Figure S383. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S384. Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
3P LOSS MUTATED	20	21	4	0
3P LOSS WILD-TYPE	11	4	9	17

Figure S384. 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 = 2.4e-05

Table S385. Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
3P LOSS MUTATED	15	20	1	7	2
3P LOSS WILD-TYPE	5	4	17	6	9

Figure S385. 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 = 2.4e-05

Table S386. Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
3P LOSS MUTATED	7	107	297
3P LOSS WILD-TYPE	321	93	57

Figure S386. 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 = 2.4e-05

Table S387. Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
3P LOSS MUTATED	13	64	138	43	5
3P LOSS WILD-TYPE	89	59	33	27	181

Figure S387. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0011

Table S388. Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
3P LOSS MUTATED	88	93	70	115
3P LOSS WILD-TYPE	94	88	117	82

Figure S388. 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 = 2.4e-05

Table S389. Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
3P LOSS MUTATED	105	1	43	87	39	38	53
3P LOSS WILD-TYPE	92	63	73	60	20	33	40

Figure S389. 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 = 2.4e-05

Table S390. Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
3P LOSS MUTATED	20	140	228	21
3P LOSS WILD-TYPE	102	59	57	252

Figure S390. 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 = 2.4e-05

Table S391. Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
3P LOSS MUTATED	10	10	121	13	94	28	84	47	2
3P LOSS WILD-TYPE	78	51	27	71	27	10	27	12	167

Figure S391. 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 = 2.4e-05

Table S392. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
3P LOSS MUTATED	28	109	260
3P LOSS WILD-TYPE	314	85	68

Figure S392. 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 = 2.4e-05

Table S393. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
3P LOSS MUTATED	9	194	186	8
3P LOSS WILD-TYPE	67	153	47	200

Figure S393. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S394. Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
3P LOSS MUTATED	8	8	14	92
3P LOSS WILD-TYPE	148	61	51	30

Figure S394. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S395. Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
3P LOSS MUTATED	5	22	0	2	25	63	5
3P LOSS WILD-TYPE	86	61	49	18	21	14	41

Figure S395. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S396. Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
3Q LOSS MUTATED	6	22	91
3Q LOSS WILD-TYPE	322	178	263

Figure S396. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S397. Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
3Q LOSS MUTATED	9	14	36	15	2
3Q LOSS WILD-TYPE	93	109	135	55	184

Figure S397. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S398. Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
3Q LOSS MUTATED	29	0	10	21	19	10	18
3Q LOSS WILD-TYPE	168	64	106	126	40	61	75

Figure S398. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S399. Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
3Q LOSS MUTATED	13	46	54	6
3Q LOSS WILD-TYPE	109	153	231	267

Figure S399. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S400. Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
3Q LOSS MUTATED	8	6	35	3	28	5	12	21	1
3Q LOSS WILD-TYPE	80	55	113	81	93	33	99	38	168

Figure S400. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S401. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
3Q LOSS MUTATED	14	26	76
3Q LOSS WILD-TYPE	328	168	252

Figure S401. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S402. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
3Q LOSS MUTATED	8	65	40	3
3Q LOSS WILD-TYPE	68	282	193	205

Figure S402. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S403. Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
3Q LOSS MUTATED	2	5	5	20
3Q LOSS WILD-TYPE	154	64	60	102

Figure S403. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0019

Table S404. Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
3Q LOSS MUTATED	2	8	0	0	4	14	4
3Q LOSS WILD-TYPE	89	75	49	20	42	63	42

Figure S404. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S405. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
4P LOSS MUTATED	20	9	69
4P LOSS WILD-TYPE	308	191	285

Figure S405. 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 = 2.4e-05

Table S406. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
4P LOSS MUTATED	5	19	21	26	4
4P LOSS WILD-TYPE	97	104	150	44	182

Figure S406. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.038

Table S407. Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
4P LOSS MUTATED	30	20	13	28
4P LOSS WILD-TYPE	152	161	174	169

Figure S407. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S408. Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
4P LOSS MUTATED	19	1	22	9	13	8	19
4P LOSS WILD-TYPE	178	63	94	138	46	63	74

Figure S408. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S409. Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
4P LOSS MUTATED	4	40	34	19
4P LOSS WILD-TYPE	118	159	251	254

Figure S409. 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 = 2.4e-05

Table S410. Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
4P LOSS MUTATED	0	17	18	12	27	4	13	5	1
4P LOSS WILD-TYPE	88	44	130	72	94	34	98	54	168

Figure S410. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0013

Table S411. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
4P LOSS MUTATED	22	32	42
4P LOSS WILD-TYPE	320	162	286

Figure S411. 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 = 2.4e-05

Table S412. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
4P LOSS MUTATED	0	60	26	10
4P LOSS WILD-TYPE	76	287	207	198

Figure S412. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0018

Table S413. Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
4P LOSS MUTATED	6	4	13	15
4P LOSS WILD-TYPE	150	65	52	107

Figure S413. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00025

Table S414. Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
4P LOSS MUTATED	4	16	0	2	7	9	0
4P LOSS WILD-TYPE	87	67	49	18	39	68	46

Figure S414. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S415. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
4Q LOSS MUTATED	20	3	69
4Q LOSS WILD-TYPE	308	197	285

Figure S415. 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 = 2.4e-05

Table S416. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
4Q LOSS MUTATED	4	17	19	26	5
4Q LOSS WILD-TYPE	98	106	152	44	181

Figure S416. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S417. Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
4Q LOSS MUTATED	18	1	23	8	13	8	14
4Q LOSS WILD-TYPE	179	63	93	139	46	63	79

Figure S417. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S418. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
4Q LOSS MUTATED	4	40	28	20
4Q LOSS WILD-TYPE	118	159	257	253

Figure S418. 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 = 2.4e-05

Table S419. Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
4Q LOSS MUTATED	0	17	16	13	27	4	10	4	1
4Q LOSS WILD-TYPE	88	44	132	71	94	34	101	55	168

Figure S419. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.0049

Table S420. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
4Q LOSS MUTATED	23	31	37
4Q LOSS WILD-TYPE	319	163	291

Figure S420. 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 = 2.4e-05

Table S421. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
4Q LOSS MUTATED	0	60	21	10
4Q LOSS WILD-TYPE	76	287	212	198

Figure S421. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0054

Table S422. Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
4Q LOSS MUTATED	7	4	13	13
4Q LOSS WILD-TYPE	149	65	52	109

Figure S422. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S423. Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
4Q LOSS MUTATED	4	17	0	2	7	7	0
4Q LOSS WILD-TYPE	87	66	49	18	39	70	46

Figure S423. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00035

Table S424. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
5P LOSS MUTATED	19	1	4
5P LOSS WILD-TYPE	309	199	350

Figure S424. 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 = 2.4e-05

Table S425. Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
5P LOSS MUTATED	13	5	0	3	1
5P LOSS WILD-TYPE	89	118	171	67	185

Figure S425. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

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

Table S426. Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
5P LOSS MUTATED	11	4	2	5
5P LOSS WILD-TYPE	171	177	185	192

Figure S426. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.064

Table S427. Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
5P LOSS MUTATED	5	3	5	0	3	1	5
5P LOSS WILD-TYPE	192	61	111	147	56	70	88

Figure S427. 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 = 2.4e-05

Table S428. Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
5P LOSS MUTATED	12	10	0	2
5P LOSS WILD-TYPE	110	189	285	271

Figure S428. 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 = 2.4e-05

Table S429. Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
5P LOSS MUTATED	11	7	0	1	4	0	0	0	1
5P LOSS WILD-TYPE	77	54	148	83	117	38	111	59	168

Figure S429. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S430. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
5P LOSS MUTATED	11	12	0	1
5P LOSS WILD-TYPE	65	335	233	207

Figure S430. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0012

Table S431. Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
5P LOSS MUTATED	2	8	5	2
5P LOSS WILD-TYPE	154	61	60	120

Figure S431. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S432. Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
5P LOSS MUTATED	1	7	0	0	1	0	8
5P LOSS WILD-TYPE	90	76	49	20	45	77	38

Figure S432. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S433. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
5Q LOSS MUTATED	19	0	4
5Q LOSS WILD-TYPE	309	200	350

Figure S433. 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 = 2.4e-05

Table S434. Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
5Q LOSS MUTATED	13	6	0	2	1
5Q LOSS WILD-TYPE	89	117	171	68	185

Figure S434. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S435. Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
5Q LOSS MUTATED	13	9	0	1
5Q LOSS WILD-TYPE	109	190	285	272

Figure S435. 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 = 2.4e-05

Table S436. Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
5Q LOSS MUTATED	11	8	0	0	3	0	0	0	1
5Q LOSS WILD-TYPE	77	53	148	84	118	38	111	59	168

Figure S436. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.039

Table S437. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
5Q LOSS MUTATED	14	6	3
5Q LOSS WILD-TYPE	328	188	325

Figure S437. 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 = 2.4e-05

Table S438. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
5Q LOSS MUTATED	11	11	0	1
5Q LOSS WILD-TYPE	65	336	233	207

Figure S438. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S439. Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
5Q LOSS MUTATED	2	8	6	2
5Q LOSS WILD-TYPE	154	61	59	120

Figure S439. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S440. Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
5Q LOSS MUTATED	1	8	0	0	1	0	8
5Q LOSS WILD-TYPE	90	75	49	20	45	77	38

Figure S440. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.01

Table S441. Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
6P LOSS MUTATED	4	10	6	1
6P LOSS WILD-TYPE	27	15	7	16

Figure S441. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.0059

Table S442. Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
6P LOSS MUTATED	3	10	1	1	6
6P LOSS WILD-TYPE	17	14	17	12	5

Figure S442. 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 = 2.4e-05

Table S443. Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
6P LOSS MUTATED	75	8	88
6P LOSS WILD-TYPE	253	192	266

Figure S443. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S444. Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
6P LOSS MUTATED	58	22	14	19	9
6P LOSS WILD-TYPE	44	101	157	51	177

Figure S444. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0015

Table S445. Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
6P LOSS MUTATED	31	33	29	61
6P LOSS WILD-TYPE	151	148	158	136

Figure S445. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S446. Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
6P LOSS MUTATED	44	12	45	17	22	4	10
6P LOSS WILD-TYPE	153	52	71	130	37	67	83

Figure S446. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S447. Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
6P LOSS MUTATED	65	62	26	16
6P LOSS WILD-TYPE	57	137	259	257

Figure S447. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S448. Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
6P LOSS MUTATED	61	16	13	4	44	6	8	11	6
6P LOSS WILD-TYPE	27	45	135	80	77	32	103	48	163

Figure S448. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S449. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
6P LOSS MUTATED	60	73	19	15
6P LOSS WILD-TYPE	16	274	214	193

Figure S449. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S450. Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
6P LOSS MUTATED	9	39	10	13
6P LOSS WILD-TYPE	147	30	55	109

Figure S450. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S451. Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
6P LOSS MUTATED	7	10	1	0	11	5	37
6P LOSS WILD-TYPE	84	73	48	20	35	72	9

Figure S451. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00822 (Fisher's exact test), Q value = 0.013

Table S452. Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
6Q LOSS MUTATED	7	11	7	1
6Q LOSS WILD-TYPE	24	14	6	16

Figure S452. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.0059

Table S453. Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
6Q LOSS MUTATED	4	11	1	3	7
6Q LOSS WILD-TYPE	16	13	17	10	4

Figure S453. 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 = 2.4e-05

Table S454. Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
6Q LOSS MUTATED	78	8	120
6Q LOSS WILD-TYPE	250	192	234

Figure S454. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S455. Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
6Q LOSS MUTATED	58	28	24	24	11
6Q LOSS WILD-TYPE	44	95	147	46	175

Figure S455. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0037

Table S456. Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
6Q LOSS MUTATED	37	45	36	68
6Q LOSS WILD-TYPE	145	136	151	129

Figure S456. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S457. Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
6Q LOSS MUTATED	55	13	48	29	23	5	13
6Q LOSS WILD-TYPE	142	51	68	118	36	66	80

Figure S457. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S458. Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
6Q LOSS MUTATED	66	65	49	24
6Q LOSS WILD-TYPE	56	134	236	249

Figure S458. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S459. Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
6Q LOSS MUTATED	61	18	22	11	44	8	22	13	5
6Q LOSS WILD-TYPE	27	43	126	73	77	30	89	46	164

Figure S459. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S460. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
6Q LOSS MUTATED	60	83	40	19
6Q LOSS WILD-TYPE	16	264	193	189

Figure S460. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S461. Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
6Q LOSS MUTATED	10	39	14	21
6Q LOSS WILD-TYPE	146	30	51	101

Figure S461. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S462. Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
6Q LOSS MUTATED	7	14	2	0	13	11	37
6Q LOSS WILD-TYPE	84	69	47	20	33	66	9

Figure S462. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.059

Table S463. Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
7P LOSS MUTATED	0	0	3	0	0	0	0
7P LOSS WILD-TYPE	197	64	113	147	59	71	93

Figure S463. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.06

Table S464. Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
7Q LOSS MUTATED	0	0	3	0	0	0	0
7Q LOSS WILD-TYPE	197	64	113	147	59	71	93

Figure S464. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S465. Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
8P LOSS MUTATED	28	28	105
8P LOSS WILD-TYPE	300	172	249

Figure S465. 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 = 2.4e-05

Table S466. Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
8P LOSS MUTATED	14	23	37	17	7
8P LOSS WILD-TYPE	88	100	134	53	179

Figure S466. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S467. Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
8P LOSS MUTATED	20	60	67	13
8P LOSS WILD-TYPE	102	139	218	260

Figure S467. 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 = 2.4e-05

Table S468. Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
8P LOSS MUTATED	16	10	38	4	44	4	23	18	3
8P LOSS WILD-TYPE	72	51	110	80	77	34	88	41	166

Figure S468. 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 = 2.4e-05

Table S469. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
8P LOSS MUTATED	30	42	86
8P LOSS WILD-TYPE	312	152	242

Figure S469. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S470. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
8P LOSS MUTATED	14	87	51	6
8P LOSS WILD-TYPE	62	260	182	202

Figure S470. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S471. Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
8P LOSS MUTATED	4	9	6	31
8P LOSS WILD-TYPE	152	60	59	91

Figure S471. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S472. Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
8P LOSS MUTATED	3	8	1	2	15	15	6
8P LOSS WILD-TYPE	88	75	48	18	31	62	40

Figure S472. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0013

Table S473. Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
8Q LOSS MUTATED	21	12	50
8Q LOSS WILD-TYPE	307	188	304

Figure S473. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S474. Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
8Q LOSS MUTATED	12	4	25	7	4
8Q LOSS WILD-TYPE	90	119	146	63	182

Figure S474. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S475. Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
8Q LOSS MUTATED	17	21	39	6
8Q LOSS WILD-TYPE	105	178	246	267

Figure S475. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S476. Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
8Q LOSS MUTATED	14	6	26	1	13	1	11	10	1
8Q LOSS WILD-TYPE	74	55	122	83	108	37	100	49	168

Figure S476. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00984 (Fisher's exact test), Q value = 0.015

Table S477. Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
8Q LOSS MUTATED	20	23	39
8Q LOSS WILD-TYPE	322	171	289

Figure S477. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S478. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
8Q LOSS MUTATED	12	38	27	5
8Q LOSS WILD-TYPE	64	309	206	203

Figure S478. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.002

Table S479. Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
8Q LOSS MUTATED	2	7	4	14
8Q LOSS WILD-TYPE	154	62	61	108

Figure S479. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0017

Table S480. Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
8Q LOSS MUTATED	2	3	0	1	9	6	6
8Q LOSS WILD-TYPE	89	80	49	19	37	71	40

Figure S480. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.026

Table S481. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
9P LOSS MUTATED	5	12	1	3
9P LOSS WILD-TYPE	26	13	12	14

Figure S481. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.032

Table S482. Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
9P LOSS MUTATED	4	12	3	1	1
9P LOSS WILD-TYPE	16	12	15	12	10

Figure S482. 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 = 2.4e-05

Table S483. Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
9P LOSS MUTATED	31	14	147
9P LOSS WILD-TYPE	297	186	207

Figure S483. 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 = 2.4e-05

Table S484. Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
9P LOSS MUTATED	16	45	24	41	7
9P LOSS WILD-TYPE	86	78	147	29	179

Figure S484. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S485. Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
9P LOSS MUTATED	48	34	24	67
9P LOSS WILD-TYPE	134	147	163	130

Figure S485. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S486. Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
9P LOSS MUTATED	40	6	40	22	29	11	25
9P LOSS WILD-TYPE	157	58	76	125	30	60	68

Figure S486. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S487. Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
9P LOSS MUTATED	18	105	37	31
9P LOSS WILD-TYPE	104	94	248	242

Figure S487. 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 = 2.4e-05

Table S488. Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
9P LOSS MUTATED	11	22	24	15	74	12	10	20	3
9P LOSS WILD-TYPE	77	39	124	69	47	26	101	39	166

Figure S488. 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 = 2.4e-05

Table S489. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
9P LOSS MUTATED	38	63	86
9P LOSS WILD-TYPE	304	131	242

Figure S489. 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 = 2.4e-05

Table S490. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
9P LOSS MUTATED	10	130	32	15
9P LOSS WILD-TYPE	66	217	201	193

Figure S490. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S491. Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
9P LOSS MUTATED	10	10	21	26
9P LOSS WILD-TYPE	146	59	44	96

Figure S491. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00021

Table S492. Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
9P LOSS MUTATED	7	24	2	4	14	10	6
9P LOSS WILD-TYPE	84	59	47	16	32	67	40

Figure S492. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.056

Table S493. Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
9Q LOSS MUTATED	5	12	2	3
9Q LOSS WILD-TYPE	26	13	11	14

Figure S493. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.056

Table S494. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
9Q LOSS MUTATED	4	12	3	1	2
9Q LOSS WILD-TYPE	16	12	15	12	9

Figure S494. 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 = 2.4e-05

Table S495. Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
9Q LOSS MUTATED	33	14	148
9Q LOSS WILD-TYPE	295	186	206

Figure S495. 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 = 2.4e-05

Table S496. Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
9Q LOSS MUTATED	19	44	23	41	6
9Q LOSS WILD-TYPE	83	79	148	29	180

Figure S496. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S497. Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
9Q LOSS MUTATED	49	35	25	67
9Q LOSS WILD-TYPE	133	146	162	130

Figure S497. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S498. Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
9Q LOSS MUTATED	43	7	41	19	30	12	24
9Q LOSS WILD-TYPE	154	57	75	128	29	59	69

Figure S498. 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 = 2.4e-05

Table S499. Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
9Q LOSS MUTATED	22	106	38	28
9Q LOSS WILD-TYPE	100	93	247	245

Figure S499. 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 = 2.4e-05

Table S500. Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
9Q LOSS MUTATED	13	22	25	15	75	12	9	20	3
9Q LOSS WILD-TYPE	75	39	123	69	46	26	102	39	166

Figure S500. 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 = 2.4e-05

Table S501. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
9Q LOSS MUTATED	41	63	85
9Q LOSS WILD-TYPE	301	131	243

Figure S501. 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 = 2.4e-05

Table S502. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
9Q LOSS MUTATED	12	132	31	14
9Q LOSS WILD-TYPE	64	215	202	194

Figure S502. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S503. Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
9Q LOSS MUTATED	11	12	21	27
9Q LOSS WILD-TYPE	145	57	44	95

Figure S503. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S504. Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
9Q LOSS MUTATED	7	23	2	4	16	11	8
9Q LOSS WILD-TYPE	84	60	47	16	30	66	38

Figure S504. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S505. Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
10P LOSS MUTATED	62	8	63
10P LOSS WILD-TYPE	266	192	291

Figure S505. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S506. Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
10P LOSS MUTATED	54	14	16	16	4
10P LOSS WILD-TYPE	48	109	155	54	182

Figure S506. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S507. Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
10P LOSS MUTATED	31	9	37	16	10	3	12
10P LOSS WILD-TYPE	166	55	79	131	49	68	81

Figure S507. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S508. Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
10P LOSS MUTATED	60	30	29	14
10P LOSS WILD-TYPE	62	169	256	259

Figure S508. 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 = 2.4e-05

Table S509. Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
10P LOSS MUTATED	58	8	17	12	21	2	9	5	1
10P LOSS WILD-TYPE	30	53	131	72	100	36	102	54	168

Figure S509. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S510. Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
10P LOSS MUTATED	71	28	32
10P LOSS WILD-TYPE	271	166	296

Figure S510. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S511. Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
10P LOSS MUTATED	57	49	18	7
10P LOSS WILD-TYPE	19	298	215	201

Figure S511. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S512. Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
10P LOSS MUTATED	3	37	10	10
10P LOSS WILD-TYPE	153	32	55	112

Figure S512. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S513. Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
10P LOSS MUTATED	1	9	1	2	6	7	34
10P LOSS WILD-TYPE	90	74	48	18	40	70	12

Figure S513. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S514. Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
10Q LOSS MUTATED	63	13	81
10Q LOSS WILD-TYPE	265	187	273

Figure S514. 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 = 2.4e-05

Table S515. Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
10Q LOSS MUTATED	56	17	23	22	4
10Q LOSS WILD-TYPE	46	106	148	48	182

Figure S515. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0016

Table S516. Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
10Q LOSS MUTATED	35	10	40	25	12	6	15
10Q LOSS WILD-TYPE	162	54	76	122	47	65	78

Figure S516. 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 = 2.4e-05

Table S517. Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
10Q LOSS MUTATED	63	40	39	15
10Q LOSS WILD-TYPE	59	159	246	258

Figure S517. 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 = 2.4e-05

Table S518. Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
10Q LOSS MUTATED	59	9	24	14	27	3	14	6	1
10Q LOSS WILD-TYPE	29	52	124	70	94	35	97	53	168

Figure S518. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S519. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
10Q LOSS MUTATED	58	64	27	6
10Q LOSS WILD-TYPE	18	283	206	202

Figure S519. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S520. Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
10Q LOSS MUTATED	3	39	12	15
10Q LOSS WILD-TYPE	153	30	53	107

Figure S520. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S521. Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
10Q LOSS MUTATED	1	12	1	2	9	9	35
10Q LOSS WILD-TYPE	90	71	48	18	37	68	11

Figure S521. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.0084

Table S522. Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
11P LOSS MUTATED	17	2	23
11P LOSS WILD-TYPE	311	198	331

Figure S522. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00019

Table S523. Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
11P LOSS MUTATED	9	8	4	11	3
11P LOSS WILD-TYPE	93	115	167	59	183

Figure S523. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0017

Table S524. Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
11P LOSS MUTATED	12	13	4	13
11P LOSS WILD-TYPE	110	186	281	260

Figure S524. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S525. Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
11P LOSS MUTATED	8	12	3	5	8	1	1	1	3
11P LOSS WILD-TYPE	80	49	145	79	113	37	110	58	166

Figure S525. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0018

Table S526. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
11P LOSS MUTATED	7	25	3	7
11P LOSS WILD-TYPE	69	322	230	201

Figure S526. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S527. Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
11P LOSS MUTATED	4	9	11	1
11P LOSS WILD-TYPE	152	60	54	121

Figure S527. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0032

Table S528. Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
11P LOSS MUTATED	3	11	1	1	3	0	6
11P LOSS WILD-TYPE	88	72	48	19	43	77	40

Figure S528. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S529. Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
11Q LOSS MUTATED	18	1	33
11Q LOSS WILD-TYPE	310	199	321

Figure S529. 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 = 2.4e-05

Table S530. Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
11Q LOSS MUTATED	9	13	4	14	4
11Q LOSS WILD-TYPE	93	110	167	56	182

Figure S530. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.0041

Table S531. Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
11Q LOSS MUTATED	6	4	13	4	9	3	8
11Q LOSS WILD-TYPE	191	60	103	143	50	68	85

Figure S531. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00023

Table S532. Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
11Q LOSS MUTATED	11	18	4	19
11Q LOSS WILD-TYPE	111	181	281	254

Figure S532. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S533. Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
11Q LOSS MUTATED	7	12	3	11	13	1	1	1	3
11Q LOSS WILD-TYPE	81	49	145	73	108	37	110	58	166

Figure S533. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00033

Table S534. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
11Q LOSS MUTATED	7	32	3	10
11Q LOSS WILD-TYPE	69	315	230	198

Figure S534. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S535. Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
11Q LOSS MUTATED	8	8	13	1
11Q LOSS WILD-TYPE	148	61	52	121

Figure S535. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00065

Table S536. Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
11Q LOSS MUTATED	6	14	1	0	3	0	6
11Q LOSS WILD-TYPE	85	69	48	20	43	77	40

Figure S536. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.01

Table S537. Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
13Q LOSS MUTATED	0	6	3	1
13Q LOSS WILD-TYPE	31	19	10	16

Figure S537. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.018

Table S538. Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
13Q LOSS MUTATED	0	6	1	0	3
13Q LOSS WILD-TYPE	20	18	17	13	8

Figure S538. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S539. Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
13Q LOSS MUTATED	68	11	58
13Q LOSS WILD-TYPE	260	189	296

Figure S539. 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 = 2.4e-05

Table S540. Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
13Q LOSS MUTATED	50	28	8	19	6
13Q LOSS WILD-TYPE	52	95	163	51	180

Figure S540. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S541. Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
13Q LOSS MUTATED	26	10	39	8	16	7	18
13Q LOSS WILD-TYPE	171	54	77	139	43	64	75

Figure S541. 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 = 2.4e-05

Table S542. Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
13Q LOSS MUTATED	55	53	15	14
13Q LOSS WILD-TYPE	67	146	270	259

Figure S542. 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 = 2.4e-05

Table S543. Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
13Q LOSS MUTATED	51	21	6	6	36	6	6	3	2
13Q LOSS WILD-TYPE	37	40	142	78	85	32	105	56	167

Figure S543. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0029

Table S544. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
13Q LOSS MUTATED	66	36	33
13Q LOSS WILD-TYPE	276	158	295

Figure S544. 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 = 2.4e-05

Table S545. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
13Q LOSS MUTATED	49	65	11	10
13Q LOSS WILD-TYPE	27	282	222	198

Figure S545. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S546. Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
13Q LOSS MUTATED	7	32	18	9
13Q LOSS WILD-TYPE	149	37	47	113

Figure S546. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S547. Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
13Q LOSS MUTATED	4	16	1	1	9	4	31
13Q LOSS WILD-TYPE	87	67	48	19	37	73	15

Figure S547. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S548. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
14Q LOSS MUTATED	8	20	2	4
14Q LOSS WILD-TYPE	23	5	11	13

Figure S548. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00021

Table S549. Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
14Q LOSS MUTATED	4	19	4	5	2
14Q LOSS WILD-TYPE	16	5	14	8	9

Figure S549. 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 = 2.4e-05

Table S550. Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
14Q LOSS MUTATED	42	30	193
14Q LOSS WILD-TYPE	286	170	161

Figure S550. 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 = 2.4e-05

Table S551. Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
14Q LOSS MUTATED	4	55	52	41	16
14Q LOSS WILD-TYPE	98	68	119	29	170

Figure S551. 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 = 2.4e-05

Table S552. Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
14Q LOSS MUTATED	59	55	32	87
14Q LOSS WILD-TYPE	123	126	155	110

Figure S552. 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 = 2.4e-05

Table S553. Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
14Q LOSS MUTATED	62	2	45	40	31	17	36
14Q LOSS WILD-TYPE	135	62	71	107	28	54	57

Figure S553. 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 = 2.4e-05

Table S554. Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
14Q LOSS MUTATED	11	116	90	45
14Q LOSS WILD-TYPE	111	83	195	228

Figure S554. 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 = 2.4e-05

Table S555. Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
14Q LOSS MUTATED	4	22	49	17	73	33	27	26	11
14Q LOSS WILD-TYPE	84	39	99	67	48	5	84	33	158

Figure S555. 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 = 2.4e-05

Table S556. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
14Q LOSS MUTATED	44	75	140
14Q LOSS WILD-TYPE	298	119	188

Figure S556. 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 = 2.4e-05

Table S557. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
14Q LOSS MUTATED	3	158	77	21
14Q LOSS WILD-TYPE	73	189	156	187

Figure S557. 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 = 2.4e-05

Table S558. Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
14Q LOSS MUTATED	17	4	21	45
14Q LOSS WILD-TYPE	139	65	44	77

Figure S558. 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 = 2.4e-05

Table S559. Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
14Q LOSS MUTATED	9	30	4	3	14	26	1
14Q LOSS WILD-TYPE	82	53	45	17	32	51	45

Figure S559. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S560. Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
15Q LOSS MUTATED	25	3	40
15Q LOSS WILD-TYPE	303	197	314

Figure S560. 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 = 2.4e-05

Table S561. Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
15Q LOSS MUTATED	4	22	5	13	9
15Q LOSS WILD-TYPE	98	101	166	57	177

Figure S561. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.00082

Table S562. Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
15Q LOSS MUTATED	11	3	18	6	12	4	8
15Q LOSS WILD-TYPE	186	61	98	141	47	67	85

Figure S562. 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 = 2.4e-05

Table S563. Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
15Q LOSS MUTATED	4	33	8	23
15Q LOSS WILD-TYPE	118	166	277	250

Figure S563. 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 = 2.4e-05

Table S564. Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
15Q LOSS MUTATED	1	17	6	9	22	2	3	1	7
15Q LOSS WILD-TYPE	87	44	142	75	99	36	108	58	162

Figure S564. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0026

Table S565. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
15Q LOSS MUTATED	1	39	10	18
15Q LOSS WILD-TYPE	75	308	223	190

Figure S565. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.0064

Table S566. Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
15Q LOSS MUTATED	13	2	13	7
15Q LOSS WILD-TYPE	143	67	52	115

Figure S566. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0038

Table S567. Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
15Q LOSS MUTATED	9	15	2	0	6	3	0
15Q LOSS WILD-TYPE	82	68	47	20	40	74	46

Figure S567. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0062

Table S568. Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
16P LOSS MUTATED	5	6	2	1	0
16P LOSS WILD-TYPE	97	117	169	69	186

Figure S568. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.015

Table S569. Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
16P LOSS MUTATED	1	0	7	4	3	0	1
16P LOSS WILD-TYPE	196	64	109	143	56	71	92

Figure S569. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00054

Table S570. Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
16P LOSS MUTATED	6	9	2	1
16P LOSS WILD-TYPE	116	190	283	272

Figure S570. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0012

Table S571. Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
16P LOSS MUTATED	3	6	1	1	5	1	1	0	0
16P LOSS WILD-TYPE	85	55	147	83	116	37	110	59	169

Figure S571. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.05

Table S572. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
16P LOSS MUTATED	5	9	4
16P LOSS WILD-TYPE	337	185	324

Figure S572. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.0078

Table S573. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
16P LOSS MUTATED	3	13	1	1
16P LOSS WILD-TYPE	73	334	232	207

Figure S573. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S574. Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
16P LOSS MUTATED	0	5	5	1
16P LOSS WILD-TYPE	156	64	60	121

Figure S574. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0065

Table S575. Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
16P LOSS MUTATED	0	4	0	0	4	0	3
16P LOSS WILD-TYPE	91	79	49	20	42	77	43

Figure S575. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.032

Table S576. Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
16Q LOSS MUTATED	8	2	18
16Q LOSS WILD-TYPE	320	198	336

Figure S576. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00088

Table S577. Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
16Q LOSS MUTATED	6	7	3	5	0
16Q LOSS WILD-TYPE	96	116	168	65	186

Figure S577. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00664 (Fisher's exact test), Q value = 0.011

Table S578. Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
16Q LOSS MUTATED	7	12	5	4
16Q LOSS WILD-TYPE	115	187	280	269

Figure S578. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0011

Table S579. Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
16Q LOSS MUTATED	4	6	3	3	9	1	2	0	0
16Q LOSS WILD-TYPE	84	55	145	81	112	37	109	59	169

Figure S579. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.002

Table S580. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
16Q LOSS MUTATED	4	19	2	2
16Q LOSS WILD-TYPE	72	328	231	206

Figure S580. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.002

Table S581. Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
16Q LOSS MUTATED	1	6	7	5
16Q LOSS WILD-TYPE	155	63	58	117

Figure S581. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00866 (Fisher's exact test), Q value = 0.014

Table S582. Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
16Q LOSS MUTATED	1	6	0	0	6	2	4
16Q LOSS WILD-TYPE	90	77	49	20	40	75	42

Figure S582. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0036

Table S583. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
17P LOSS MUTATED	0	5	5	2
17P LOSS WILD-TYPE	31	20	8	15

Figure S583. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.0052

Table S584. Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17P LOSS MUTATED	0	5	2	0	5
17P LOSS WILD-TYPE	20	19	16	13	6

Figure S584. 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 = 2.4e-05

Table S585. Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
17P LOSS MUTATED	63	5	43
17P LOSS WILD-TYPE	265	195	311

Figure S585. 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 = 2.4e-05

Table S586. Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
17P LOSS MUTATED	59	8	2	13	2
17P LOSS WILD-TYPE	43	115	169	57	184

Figure S586. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S587. Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
17P LOSS MUTATED	21	12	35	8	8	4	9
17P LOSS WILD-TYPE	176	52	81	139	51	67	84

Figure S587. 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 = 2.4e-05

Table S588. Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
17P LOSS MUTATED	67	28	6	10
17P LOSS WILD-TYPE	55	171	279	263

Figure S588. 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 = 2.4e-05

Table S589. Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
17P LOSS MUTATED	61	8	3	9	24	2	3	1	0
17P LOSS WILD-TYPE	27	53	145	75	97	36	108	58	169

Figure S589. 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 = 2.4e-05

Table S590. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
17P LOSS MUTATED	69	21	21
17P LOSS WILD-TYPE	273	173	307

Figure S590. 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 = 2.4e-05

Table S591. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
17P LOSS MUTATED	60	42	6	3
17P LOSS WILD-TYPE	16	305	227	205

Figure S591. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S592. Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
17P LOSS MUTATED	3	37	12	6
17P LOSS WILD-TYPE	153	32	53	116

Figure S592. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S593. Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
17P LOSS MUTATED	1	12	0	0	7	2	36
17P LOSS WILD-TYPE	90	71	49	20	39	75	10

Figure S593. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00067

Table S594. Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
17Q LOSS MUTATED	0	4	5	0
17Q LOSS WILD-TYPE	31	21	8	17

Figure S594. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 7e-04

Table S595. Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17Q LOSS MUTATED	0	4	0	0	5
17Q LOSS WILD-TYPE	20	20	18	13	6

Figure S595. 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 = 2.4e-05

Table S596. Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
17Q LOSS MUTATED	55	5	22
17Q LOSS WILD-TYPE	273	195	332

Figure S596. 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 = 2.4e-05

Table S597. Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
17Q LOSS MUTATED	55	3	1	4	1
17Q LOSS WILD-TYPE	47	120	170	66	185

Figure S597. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S598. Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
17Q LOSS MUTATED	19	11	29	6	3	1	4
17Q LOSS WILD-TYPE	178	53	87	141	56	70	89

Figure S598. 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 = 2.4e-05

Table S599. Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
17Q LOSS MUTATED	62	15	4	1
17Q LOSS WILD-TYPE	60	184	281	272

Figure S599. 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 = 2.4e-05

Table S600. Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
17Q LOSS MUTATED	61	2	1	1	13	1	2	1	0
17Q LOSS WILD-TYPE	27	59	147	83	108	37	109	58	169

Figure S600. 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 = 2.4e-05

Table S601. Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
17Q LOSS MUTATED	62	6	14
17Q LOSS WILD-TYPE	280	188	314

Figure S601. 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 = 2.4e-05

Table S602. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
17Q LOSS MUTATED	60	17	4	1
17Q LOSS WILD-TYPE	16	330	229	207

Figure S602. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S603. Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
17Q LOSS MUTATED	1	36	2	3
17Q LOSS WILD-TYPE	155	33	63	119

Figure S603. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S604. Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
17Q LOSS MUTATED	0	2	0	0	3	1	36
17Q LOSS WILD-TYPE	91	81	49	20	43	76	10

Figure S604. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S605. Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
18P LOSS MUTATED	42	7	92
18P LOSS WILD-TYPE	286	193	262

Figure S605. 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 = 2.4e-05

Table S606. Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
18P LOSS MUTATED	11	39	12	24	17
18P LOSS WILD-TYPE	91	84	159	46	169

Figure S606. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00077

Table S607. Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
18P LOSS MUTATED	35	15	26	46
18P LOSS WILD-TYPE	147	166	161	151

Figure S607. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S608. Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
18P LOSS MUTATED	19	8	34	13	23	8	17
18P LOSS WILD-TYPE	178	56	82	134	36	63	76

Figure S608. 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 = 2.4e-05

Table S609. Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
18P LOSS MUTATED	11	76	16	37
18P LOSS WILD-TYPE	111	123	269	236

Figure S609. 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 = 2.4e-05

Table S610. Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
18P LOSS MUTATED	10	17	6	21	50	10	6	10	10
18P LOSS WILD-TYPE	78	44	142	63	71	28	105	49	159

Figure S610. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0033

Table S611. Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
18P LOSS MUTATED	44	48	49
18P LOSS WILD-TYPE	298	146	279

Figure S611. 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 = 2.4e-05

Table S612. Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
18P LOSS MUTATED	9	98	14	20
18P LOSS WILD-TYPE	67	249	219	188

Figure S612. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S613. Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
18P LOSS MUTATED	17	10	25	11
18P LOSS WILD-TYPE	139	59	40	111

Figure S613. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S614. Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
18P LOSS MUTATED	12	25	2	2	11	4	7
18P LOSS WILD-TYPE	79	58	47	18	35	73	39

Figure S614. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S615. Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
18Q LOSS MUTATED	44	10	94
18Q LOSS WILD-TYPE	284	190	260

Figure S615. 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 = 2.4e-05

Table S616. Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
18Q LOSS MUTATED	13	40	13	26	16
18Q LOSS WILD-TYPE	89	83	158	44	170

Figure S616. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0013

Table S617. Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	182	181	187	197
18Q LOSS MUTATED	38	17	27	47
18Q LOSS WILD-TYPE	144	164	160	150

Figure S617. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S618. Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
18Q LOSS MUTATED	18	8	35	16	24	8	20
18Q LOSS WILD-TYPE	179	56	81	131	35	63	73

Figure S618. 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 = 2.4e-05

Table S619. Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
18Q LOSS MUTATED	14	77	16	40
18Q LOSS WILD-TYPE	108	122	269	233

Figure S619. 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 = 2.4e-05

Table S620. Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
18Q LOSS MUTATED	11	19	7	25	49	10	6	11	9
18Q LOSS WILD-TYPE	77	42	141	59	72	28	105	48	160

Figure S620. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.013

Table S621. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
18Q LOSS MUTATED	50	48	50
18Q LOSS WILD-TYPE	292	146	278

Figure S621. 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 = 2.4e-05

Table S622. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
18Q LOSS MUTATED	10	102	16	20
18Q LOSS WILD-TYPE	66	245	217	188

Figure S622. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S623. Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
18Q LOSS MUTATED	17	12	28	11
18Q LOSS WILD-TYPE	139	57	37	111

Figure S623. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S624. Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
18Q LOSS MUTATED	12	29	2	2	11	4	8
18Q LOSS WILD-TYPE	79	54	47	18	35	73	38

Figure S624. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.002

Table S625. Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
19P LOSS MUTATED	11	0	18
19P LOSS WILD-TYPE	317	200	336

Figure S625. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

Table S626. Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
19P LOSS MUTATED	1	5	1	9	8
19P LOSS WILD-TYPE	101	118	170	61	178

Figure S626. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0011

Table S627. Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
19P LOSS MUTATED	1	10	2	16
19P LOSS WILD-TYPE	121	189	283	257

Figure S627. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00044

Table S628. Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
19P LOSS MUTATED	1	7	1	7	7	0	1	0	5
19P LOSS WILD-TYPE	87	54	147	77	114	38	110	59	164

Figure S628. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.035

Table S629. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
19P LOSS MUTATED	1	17	2	9
19P LOSS WILD-TYPE	75	330	231	199

Figure S629. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0015

Table S630. Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
19P LOSS MUTATED	8	1	9	1
19P LOSS WILD-TYPE	148	68	56	121

Figure S630. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.006

Table S631. Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
19Q LOSS MUTATED	8	0	15
19Q LOSS WILD-TYPE	320	200	339

Figure S631. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0017

Table S632. Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
19Q LOSS MUTATED	2	3	0	7	7
19Q LOSS WILD-TYPE	100	120	171	63	179

Figure S632. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0037

Table S633. Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
19Q LOSS MUTATED	2	6	1	14
19Q LOSS WILD-TYPE	120	193	284	259

Figure S633. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0013

Table S634. Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
19Q LOSS MUTATED	2	7	0	5	3	0	1	0	5
19Q LOSS WILD-TYPE	86	54	148	79	118	38	110	59	164

Figure S634. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.0076

Table S635. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
19Q LOSS MUTATED	15	6	2
19Q LOSS WILD-TYPE	327	188	326

Figure S635. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.058

Table S636. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
19Q LOSS MUTATED	2	12	1	8
19Q LOSS WILD-TYPE	74	335	232	200

Figure S636. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0026

Table S637. Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
19Q LOSS MUTATED	9	2	7	0
19Q LOSS WILD-TYPE	147	67	58	122

Figure S637. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00714 (Fisher's exact test), Q value = 0.011

Table S638. Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
20P LOSS MUTATED	5	1	1	1	0
20P LOSS WILD-TYPE	97	122	170	69	186

Figure S638. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00082

Table S639. Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
20P LOSS MUTATED	4	7	1	0
20P LOSS WILD-TYPE	118	192	284	273

Figure S639. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.022

Table S640. Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
20P LOSS MUTATED	4	1	1	0	3	1	0	2	0
20P LOSS WILD-TYPE	84	60	147	84	118	37	111	57	169

Figure S640. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00378 (Fisher's exact test), Q value = 0.0062

Table S641. Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
20P LOSS MUTATED	4	7	1	0
20P LOSS WILD-TYPE	72	340	232	208

Figure S641. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.0097

Table S642. Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
20P LOSS MUTATED	0	4	1	1
20P LOSS WILD-TYPE	156	65	64	121

Figure S642. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.021

Table S643. Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
20P LOSS MUTATED	0	1	0	0	0	1	4
20P LOSS WILD-TYPE	91	82	49	20	46	76	42

Figure S643. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.0081

Table S644. Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
20Q LOSS MUTATED	3	0	0	0	0
20Q LOSS WILD-TYPE	99	123	171	70	186

Figure S644. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.0046

Table S645. Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
20Q LOSS MUTATED	3	3	0	0
20Q LOSS WILD-TYPE	119	196	285	273

Figure S645. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.022

Table S646. Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
20Q LOSS MUTATED	3	0	0	0	1	1	0	1	0
20Q LOSS WILD-TYPE	85	61	148	84	120	37	111	58	169

Figure S646. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00585 (Fisher's exact test), Q value = 0.0095

Table S647. Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
20Q LOSS MUTATED	3	3	0	0
20Q LOSS WILD-TYPE	73	344	233	208

Figure S647. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.014

Table S648. Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
20Q LOSS MUTATED	0	3	0	0
20Q LOSS WILD-TYPE	156	66	65	122

Figure S648. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.0094

Table S649. Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
20Q LOSS MUTATED	0	0	0	0	0	0	3
20Q LOSS WILD-TYPE	91	83	49	20	46	77	43

Figure S649. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.039

Table S650. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
21Q LOSS MUTATED	1	2	4	4
21Q LOSS WILD-TYPE	30	23	9	13

Figure S650. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.036

Table S651. Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
21Q LOSS MUTATED	0	2	4	1	4
21Q LOSS WILD-TYPE	20	22	14	12	7

Figure S651. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S652. Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
21Q LOSS MUTATED	83	9	41
21Q LOSS WILD-TYPE	245	191	313

Figure S652. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S653. Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
21Q LOSS MUTATED	40	19	12	17	21
21Q LOSS WILD-TYPE	62	104	159	53	165

Figure S653. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S654. Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
21Q LOSS MUTATED	23	13	36	12	14	7	9
21Q LOSS WILD-TYPE	174	51	80	135	45	64	84

Figure S654. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S655. Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
21Q LOSS MUTATED	50	24	17	40
21Q LOSS WILD-TYPE	72	175	268	233

Figure S655. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S656. Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
21Q LOSS MUTATED	46	16	9	11	13	2	7	5	22
21Q LOSS WILD-TYPE	42	45	139	73	108	36	104	54	147

Figure S656. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S657. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
21Q LOSS MUTATED	79	29	24
21Q LOSS WILD-TYPE	263	165	304

Figure S657. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S658. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
21Q LOSS MUTATED	45	44	12	31
21Q LOSS WILD-TYPE	31	303	221	177

Figure S658. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S659. Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
21Q LOSS MUTATED	24	27	14	11
21Q LOSS WILD-TYPE	132	42	51	111

Figure S659. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S660. Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
21Q LOSS MUTATED	16	18	3	0	6	7	26
21Q LOSS WILD-TYPE	75	65	46	20	40	70	20

Figure S660. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.011

Table S661. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
22Q LOSS MUTATED	0	4	1	5
22Q LOSS WILD-TYPE	31	21	12	12

Figure S661. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.054

Table S662. Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
22Q LOSS MUTATED	0	4	5	0	1
22Q LOSS WILD-TYPE	20	20	13	13	10

Figure S662. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S663. Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
22Q LOSS MUTATED	50	4	53
22Q LOSS WILD-TYPE	278	196	301

Figure S663. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S664. Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
22Q LOSS MUTATED	16	18	4	27	24
22Q LOSS WILD-TYPE	86	105	167	43	162

Figure S664. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S665. Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
22Q LOSS MUTATED	16	14	17	8	15	5	17
22Q LOSS WILD-TYPE	181	50	99	139	44	66	76

Figure S665. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S666. Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
22Q LOSS MUTATED	15	31	7	54
22Q LOSS WILD-TYPE	107	168	278	219

Figure S666. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S667. Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
22Q LOSS MUTATED	10	18	8	33	19	3	1	3	12
22Q LOSS WILD-TYPE	78	43	140	51	102	35	110	56	157

Figure S667. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S668. Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
22Q LOSS MUTATED	64	19	24
22Q LOSS WILD-TYPE	278	175	304

Figure S668. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S669. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
22Q LOSS MUTATED	9	58	8	32
22Q LOSS WILD-TYPE	67	289	225	176

Figure S669. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00063

Table S670. Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
22Q LOSS MUTATED	29	12	16	6
22Q LOSS WILD-TYPE	127	57	49	116

Figure S670. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S671. Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
22Q LOSS MUTATED	19	23	2	5	3	3	8
22Q LOSS WILD-TYPE	72	60	47	15	43	74	38

Figure S671. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.044

Table S672. Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	25	13	17
XP LOSS MUTATED	3	1	5	3
XP LOSS WILD-TYPE	28	24	8	14

Figure S672. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.045

Table S673. Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
XP LOSS MUTATED	2	1	3	1	5
XP LOSS WILD-TYPE	18	23	15	12	6

Figure S673. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S674. Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
XP LOSS MUTATED	62	10	42
XP LOSS WILD-TYPE	266	190	312

Figure S674. 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 = 2.4e-05

Table S675. Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
XP LOSS MUTATED	48	8	11	18	8
XP LOSS WILD-TYPE	54	115	160	52	178

Figure S675. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S676. Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
XP LOSS MUTATED	29	9	28	10	3	3	14
XP LOSS WILD-TYPE	168	55	88	137	56	68	79

Figure S676. 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 = 2.4e-05

Table S677. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
XP LOSS MUTATED	54	15	19	26
XP LOSS WILD-TYPE	68	184	266	247

Figure S677. 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 = 2.4e-05

Table S678. Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
XP LOSS MUTATED	49	15	6	15	7	4	7	7	4
XP LOSS WILD-TYPE	39	46	142	69	114	34	104	52	165

Figure S678. 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 = 2.4e-05

Table S679. Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
XP LOSS MUTATED	74	15	24
XP LOSS WILD-TYPE	268	179	304

Figure S679. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S680. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
XP LOSS MUTATED	47	40	13	13
XP LOSS WILD-TYPE	29	307	220	195

Figure S680. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S681. Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
XP LOSS MUTATED	8	34	13	6
XP LOSS WILD-TYPE	148	35	52	116

Figure S681. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S682. Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
XP LOSS MUTATED	5	18	1	3	3	2	29
XP LOSS WILD-TYPE	86	65	48	17	43	75	17

Figure S682. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S683. Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	200	354
XQ LOSS MUTATED	63	8	42
XQ LOSS WILD-TYPE	265	192	312

Figure S683. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S684. Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	102	123	171	70	186
XQ LOSS MUTATED	47	8	10	18	8
XQ LOSS WILD-TYPE	55	115	161	52	178

Figure S684. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S685. Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	197	64	116	147	59	71	93
XQ LOSS MUTATED	28	9	31	8	4	3	13
XQ LOSS WILD-TYPE	169	55	85	139	55	68	80

Figure S685. 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 = 2.4e-05

Table S686. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	199	285	273
XQ LOSS MUTATED	53	19	16	25
XQ LOSS WILD-TYPE	69	180	269	248

Figure S686. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S687. Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	88	61	148	84	121	38	111	59	169
XQ LOSS MUTATED	48	16	5	15	10	3	6	6	4
XQ LOSS WILD-TYPE	40	45	143	69	111	35	105	53	165

Figure S687. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S688. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	342	194	328
XQ LOSS MUTATED	71	17	24
XQ LOSS WILD-TYPE	271	177	304

Figure S688. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S689. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	347	233	208
XQ LOSS MUTATED	46	44	11	11
XQ LOSS WILD-TYPE	30	303	222	197

Figure S689. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S690. Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	69	65	122
XQ LOSS MUTATED	7	33	14	6
XQ LOSS WILD-TYPE	149	36	51	116

Figure S690. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S691. Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	91	83	49	20	46	77	46
XQ LOSS MUTATED	5	16	1	3	5	2	28
XQ LOSS WILD-TYPE	86	67	48	17	41	75	18

Figure S691. 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/KIPAN-TP/22533780/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/22570984/KIPAN-TP.transferedmergedcluster.txt
Number of patients = 882
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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