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 80 arm-level events and 12 molecular subtypes across 1079 patients, 567 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 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, 567 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
1p gain	205 (19%)	874	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00021 (0.0932)
2p gain	123 (11%)	956	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00014 (0.0655)
10p gain	214 (20%)	865	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
4p loss	353 (33%)	726	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	5e-05 (0.0246)
5p loss	140 (13%)	939	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
5q loss	228 (21%)	851	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
9q loss	282 (26%)	797	0.0001 (0.0477)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00031 (0.132)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
12q loss	131 (12%)	948	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00018 (0.081)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
14q loss	266 (25%)	813	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
2q gain	73 (7%)	1006	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0939 (1.00)
6p gain	207 (19%)	872	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00014 (0.0655)	0.00129 (0.461)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
6q gain	149 (14%)	930	1e-05 (0.0096)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00456 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
18p gain	177 (16%)	902	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00098 (0.369)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0154)
21q gain	195 (18%)	884	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0003 (0.128)	0.00064 (0.252)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
16q loss	593 (55%)	486	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00034 (0.143)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00121 (0.443)	7e-05 (0.0337)
17q loss	275 (25%)	804	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	0.00258 (0.838)
19p loss	193 (18%)	886	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0275 (1.00)	0.00014 (0.0655)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
3q gain	212 (20%)	867	0.00043 (0.175)	0.00017 (0.0775)	1e-05 (0.0096)	1e-05 (0.0096)	0.0228 (1.00)	0.0381 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00021 (0.0932)
8q gain	528 (49%)	551	2e-05 (0.011)	3e-05 (0.0154)	1e-05 (0.0096)	1e-05 (0.0096)	0.0736 (1.00)	0.214 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
9p gain	141 (13%)	938	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00718 (1.00)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00046 (0.187)	0.115 (1.00)
20q gain	450 (42%)	629	5e-05 (0.0246)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0697 (1.00)	0.133 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00017 (0.0775)
22q gain	98 (9%)	981	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00053 (0.213)	2e-05 (0.011)	0.00082 (0.317)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00034 (0.143)	0.00612 (1.00)
3p loss	186 (17%)	893	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00174 (0.597)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00681 (1.00)
4q loss	312 (29%)	767	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00053 (0.213)	0.00266 (0.857)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0076 (1.00)
9p loss	312 (29%)	767	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00248 (0.813)	0.00837 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00012 (0.0565)	1e-05 (0.0096)
13q loss	432 (40%)	647	5e-05 (0.0246)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.297 (1.00)	0.00077 (0.301)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00041 (0.169)
15q loss	319 (30%)	760	5e-05 (0.0246)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00273 (0.876)	0.00609 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0154)
17p loss	579 (54%)	500	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0154)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0751 (1.00)	0.121 (1.00)
16p gain	463 (43%)	616	0.00011 (0.0522)	0.00128 (0.458)	1e-05 (0.0096)	1e-05 (0.0096)	0.0156 (1.00)	1e-05 (0.0096)	2e-05 (0.011)	2e-05 (0.011)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	0.00345 (1.00)
8p loss	399 (37%)	680	3e-05 (0.0154)	0.00018 (0.081)	1e-05 (0.0096)	2e-05 (0.011)	0.148 (1.00)	0.00035 (0.146)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	3e-05 (0.0154)	0.00118 (0.435)	0.00091 (0.346)
19q loss	161 (15%)	918	0.0052 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.124 (1.00)	0.00491 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00021 (0.0932)	1e-05 (0.0096)
20p loss	93 (9%)	986	0.00317 (1.00)	9e-05 (0.043)	1e-05 (0.0096)	1e-05 (0.0096)	0.111 (1.00)	0.174 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	8e-05 (0.0383)
17q gain	216 (20%)	863	1e-05 (0.0096)	0.00014 (0.0655)	1e-05 (0.0096)	0.00012 (0.0565)	0.531 (1.00)	0.00013 (0.061)	1e-05 (0.0096)	1e-05 (0.0096)	0.194 (1.00)	0.00023 (0.101)	0.00112 (0.416)	0.00173 (0.595)
18q gain	153 (14%)	926	1e-05 (0.0096)	5e-05 (0.0246)	1e-05 (0.0096)	5e-05 (0.0246)	0.0761 (1.00)	0.00178 (0.607)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00103 (0.385)	0.00182 (0.613)
20p gain	415 (38%)	664	3e-05 (0.0154)	2e-05 (0.011)	1e-05 (0.0096)	0.00376 (1.00)	0.00506 (1.00)	0.334 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.011)	0.00502 (1.00)
2p loss	181 (17%)	898	0.0081 (1.00)	0.0123 (1.00)	1e-05 (0.0096)	0.00046 (0.187)	0.0012 (0.44)	0.00055 (0.218)	1e-05 (0.0096)	1e-05 (0.0096)	4e-05 (0.02)	0.00032 (0.135)	1e-05 (0.0096)	0.0512 (1.00)
12p loss	151 (14%)	928	0.00178 (0.607)	0.00155 (0.539)	1e-05 (0.0096)	1e-05 (0.0096)	0.0196 (1.00)	0.00775 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
20q loss	55 (5%)	1024	0.0118 (1.00)	0.00518 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.14 (1.00)	0.0402 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00021 (0.0932)
5q gain	211 (20%)	868	0.0109 (1.00)	0.00607 (1.00)	1e-05 (0.0096)	0.00051 (0.206)	0.00152 (0.53)	0.00015 (0.0691)	0.00062 (0.244)	0.0002 (0.0892)	0.00188 (0.632)	1e-05 (0.0096)	0.00041 (0.169)	0.0464 (1.00)
xq gain	140 (13%)	939	0.00034 (0.143)	0.0009 (0.343)	1e-05 (0.0096)	2e-05 (0.011)	0.457 (1.00)	0.177 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00073 (0.286)	0.0083 (1.00)
10q loss	229 (21%)	850	0.00288 (0.919)	0.00887 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.0022 (0.724)	0.0456 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00027 (0.117)	1e-05 (0.0096)	0.0001 (0.0477)	0.0102 (1.00)
11p loss	275 (25%)	804	0.00372 (1.00)	0.0164 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.0236 (1.00)	0.00032 (0.135)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0154)	1e-05 (0.0096)	0.00341 (1.00)	0.00404 (1.00)
18p loss	320 (30%)	759	0.00029 (0.125)	0.00042 (0.172)	1e-05 (0.0096)	1e-05 (0.0096)	0.205 (1.00)	0.276 (1.00)	0.00039 (0.161)	1e-05 (0.0096)	0.00516 (1.00)	2e-05 (0.011)	0.392 (1.00)	0.94 (1.00)
18q loss	321 (30%)	758	0.00025 (0.109)	0.00014 (0.0655)	1e-05 (0.0096)	1e-05 (0.0096)	0.0499 (1.00)	0.11 (1.00)	2e-05 (0.011)	1e-05 (0.0096)	0.00433 (1.00)	1e-05 (0.0096)	0.205 (1.00)	0.612 (1.00)
10q gain	124 (11%)	955	0.0323 (1.00)	0.00107 (0.399)	1e-05 (0.0096)	0.00315 (0.999)	0.0233 (1.00)	0.0611 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00014 (0.0655)	0.00251 (0.821)
11q gain	94 (9%)	985	0.181 (1.00)	0.0476 (1.00)	1e-05 (0.0096)	0.00055 (0.218)	0.827 (1.00)	0.76 (1.00)	2e-05 (0.011)	0.00017 (0.0775)	3e-05 (0.0154)	0.0003 (0.128)	0.0573 (1.00)	0.0421 (1.00)
12p gain	227 (21%)	852	0.00087 (0.332)	4e-05 (0.02)	1e-05 (0.0096)	0.00129 (0.461)	0.102 (1.00)	0.0184 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00015 (0.0691)	0.00118 (0.435)	0.0195 (1.00)
19p gain	189 (18%)	890	0.00025 (0.109)	0.00559 (1.00)	1e-05 (0.0096)	0.0134 (1.00)	0.00786 (1.00)	0.0292 (1.00)	1e-05 (0.0096)	4e-05 (0.02)	2e-05 (0.011)	0.00018 (0.081)	0.0167 (1.00)	0.416 (1.00)
1p loss	243 (23%)	836	0.00161 (0.559)	2e-05 (0.011)	1e-05 (0.0096)	1e-05 (0.0096)	0.499 (1.00)	0.437 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.0179 (1.00)	1e-05 (0.0096)	0.0018 (0.61)	0.698 (1.00)
7p loss	111 (10%)	968	0.0203 (1.00)	0.001 (0.376)	1e-05 (0.0096)	0.00086 (0.329)	0.143 (1.00)	0.0334 (1.00)	1e-05 (0.0096)	4e-05 (0.02)	1e-05 (0.0096)	1e-05 (0.0096)	0.0008 (0.311)	0.00016 (0.0733)
11q loss	364 (34%)	715	4e-05 (0.02)	6e-05 (0.029)	1e-05 (0.0096)	2e-05 (0.011)	0.906 (1.00)	0.00253 (0.825)	0.00017 (0.0775)	1e-05 (0.0096)	0.0497 (1.00)	0.00672 (1.00)	0.0117 (1.00)	0.0289 (1.00)
3p gain	135 (13%)	944	0.0271 (1.00)	0.0439 (1.00)	1e-05 (0.0096)	0.00017 (0.0775)	0.476 (1.00)	0.0678 (1.00)	1e-05 (0.0096)	3e-05 (0.0154)	0.0118 (1.00)	6e-05 (0.029)	0.0778 (1.00)	0.207 (1.00)
7q gain	266 (25%)	813	0.00334 (1.00)	0.027 (1.00)	1e-05 (0.0096)	2e-05 (0.011)	0.0837 (1.00)	0.295 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00411 (1.00)	3e-05 (0.0154)	0.00597 (1.00)	0.567 (1.00)
13q gain	92 (9%)	987	0.22 (1.00)	0.282 (1.00)	1e-05 (0.0096)	0.0242 (1.00)	0.0219 (1.00)	0.138 (1.00)	4e-05 (0.02)	1e-05 (0.0096)	0.00027 (0.117)	0.00045 (0.183)	0.0815 (1.00)	0.0255 (1.00)
19q gain	222 (21%)	857	0.00108 (0.402)	0.00379 (1.00)	1e-05 (0.0096)	0.00203 (0.674)	0.00451 (1.00)	0.0512 (1.00)	2e-05 (0.011)	2e-05 (0.011)	1e-05 (0.0096)	3e-05 (0.0154)	0.0158 (1.00)	0.0707 (1.00)
2q loss	210 (19%)	869	0.0877 (1.00)	0.0282 (1.00)	1e-05 (0.0096)	0.0418 (1.00)	0.00082 (0.317)	0.00205 (0.679)	3e-05 (0.0154)	1e-05 (0.0096)	0.00061 (0.241)	0.00167 (0.578)	0.00027 (0.117)	0.0747 (1.00)
3q loss	103 (10%)	976	0.00123 (0.448)	0.00024 (0.105)	1e-05 (0.0096)	0.00151 (0.528)	0.28 (1.00)	0.0131 (1.00)	0.0008 (0.311)	2e-05 (0.011)	3e-05 (0.0154)	0.00018 (0.081)	0.0834 (1.00)	0.0756 (1.00)
xq loss	185 (17%)	894	0.155 (1.00)	0.0026 (0.842)	1e-05 (0.0096)	1e-05 (0.0096)	0.041 (1.00)	0.0154 (1.00)	0.00011 (0.0522)	1e-05 (0.0096)	0.00037 (0.154)	0.00143 (0.503)	0.00668 (1.00)	0.00599 (1.00)
4p gain	76 (7%)	1003	0.00053 (0.213)	0.00127 (0.457)	1e-05 (0.0096)	0.0281 (1.00)	0.74 (1.00)	0.162 (1.00)	0.0103 (1.00)	3e-05 (0.0154)	0.486 (1.00)	0.00039 (0.161)	0.315 (1.00)	0.0929 (1.00)
4q gain	73 (7%)	1006	2e-05 (0.011)	0.00021 (0.0932)	1e-05 (0.0096)	0.0127 (1.00)	0.243 (1.00)	0.0225 (1.00)	0.015 (1.00)	1e-05 (0.0096)	0.49 (1.00)	0.0119 (1.00)	0.105 (1.00)	0.0212 (1.00)
7p gain	309 (29%)	770	0.0069 (1.00)	0.129 (1.00)	1e-05 (0.0096)	3e-05 (0.0154)	0.657 (1.00)	0.75 (1.00)	0.00017 (0.0775)	4e-05 (0.02)	0.0759 (1.00)	0.0193 (1.00)	0.0752 (1.00)	0.724 (1.00)
8p gain	289 (27%)	790	0.181 (1.00)	0.11 (1.00)	1e-05 (0.0096)	0.00034 (0.143)	0.773 (1.00)	0.0215 (1.00)	0.00052 (0.209)	1e-05 (0.0096)	0.0172 (1.00)	0.0467 (1.00)	0.00527 (1.00)	0.114 (1.00)
11p gain	137 (13%)	942	0.789 (1.00)	0.0812 (1.00)	1e-05 (0.0096)	0.00386 (1.00)	0.966 (1.00)	0.728 (1.00)	0.00053 (0.213)	0.00085 (0.327)	6e-05 (0.029)	0.00143 (0.503)	0.00357 (1.00)	0.00029 (0.125)
14q gain	143 (13%)	936	0.00121 (0.443)	0.0139 (1.00)	1e-05 (0.0096)	0.0019 (0.636)	0.498 (1.00)	0.234 (1.00)	5e-05 (0.0246)	2e-05 (0.011)	0.292 (1.00)	1e-05 (0.0096)	0.00138 (0.487)	0.321 (1.00)
6q loss	276 (26%)	803	0.00031 (0.132)	0.0126 (1.00)	1e-05 (0.0096)	0.00989 (1.00)	0.185 (1.00)	0.0673 (1.00)	0.00028 (0.121)	0.00011 (0.0522)	0.099 (1.00)	0.00091 (0.346)	0.00982 (1.00)	0.363 (1.00)
7q loss	119 (11%)	960	0.0371 (1.00)	0.00177 (0.605)	2e-05 (0.011)	0.0605 (1.00)	0.686 (1.00)	0.492 (1.00)	0.0002 (0.0892)	0.00197 (0.656)	1e-05 (0.0096)	2e-05 (0.011)	0.0251 (1.00)	0.00462 (1.00)
10p loss	173 (16%)	906	0.282 (1.00)	0.232 (1.00)	1e-05 (0.0096)	0.00014 (0.0655)	0.32 (1.00)	0.479 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.153 (1.00)	0.00181 (0.612)	0.201 (1.00)	0.61 (1.00)
16p loss	173 (16%)	906	0.218 (1.00)	0.0973 (1.00)	0.00011 (0.0522)	0.0148 (1.00)	0.0256 (1.00)	0.0762 (1.00)	0.00126 (0.456)	0.0003 (0.128)	5e-05 (0.0246)	0.00077 (0.301)	0.00022 (0.0966)	0.03 (1.00)
1q gain	706 (65%)	373	0.00131 (0.465)	0.00572 (1.00)	1e-05 (0.0096)	0.0703 (1.00)	0.602 (1.00)	0.292 (1.00)	0.966 (1.00)	2e-05 (0.011)	0.913 (1.00)	0.0005 (0.202)	0.12 (1.00)	0.214 (1.00)
12q gain	190 (18%)	889	0.00127 (0.457)	0.00137 (0.485)	1e-05 (0.0096)	0.00405 (1.00)	0.284 (1.00)	0.11 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.216 (1.00)	0.0221 (1.00)	0.00126 (0.456)	0.708 (1.00)
22q loss	482 (45%)	597	0.0539 (1.00)	0.00569 (1.00)	1e-05 (0.0096)	0.0542 (1.00)	0.0217 (1.00)	0.00091 (0.346)	7e-05 (0.0337)	1e-05 (0.0096)	0.0372 (1.00)	0.00283 (0.906)	0.00342 (1.00)	0.149 (1.00)
6p loss	188 (17%)	891	0.0239 (1.00)	0.161 (1.00)	1e-05 (0.0096)	0.173 (1.00)	0.586 (1.00)	0.0373 (1.00)	0.00033 (0.139)	0.00301 (0.957)	0.308 (1.00)	0.0892 (1.00)	0.00669 (1.00)	0.528 (1.00)
5p gain	315 (29%)	764	0.021 (1.00)	0.0411 (1.00)	1e-05 (0.0096)	0.00706 (1.00)	0.97 (1.00)	0.112 (1.00)	0.268 (1.00)	0.0248 (1.00)	0.182 (1.00)	0.0755 (1.00)	0.243 (1.00)	0.311 (1.00)
9q gain	119 (11%)	960	0.273 (1.00)	0.00101 (0.379)	1e-05 (0.0096)	0.144 (1.00)	0.876 (1.00)	0.148 (1.00)	0.00658 (1.00)	0.0144 (1.00)	0.0699 (1.00)	0.0369 (1.00)	0.0971 (1.00)	0.0471 (1.00)
15q gain	87 (8%)	992	0.0416 (1.00)	0.279 (1.00)	0.00015 (0.0691)	0.0354 (1.00)	0.49 (1.00)	0.0623 (1.00)	0.00532 (1.00)	0.00085 (0.327)	0.352 (1.00)	0.00521 (1.00)	0.504 (1.00)	0.133 (1.00)
16q gain	141 (13%)	938	0.482 (1.00)	0.403 (1.00)	0.00641 (1.00)	0.02 (1.00)	0.351 (1.00)	0.603 (1.00)	0.0573 (1.00)	0.00401 (1.00)	0.00488 (1.00)	0.00016 (0.0733)	0.133 (1.00)	0.248 (1.00)
17p gain	106 (10%)	973	0.03 (1.00)	0.329 (1.00)	1e-05 (0.0096)	0.0303 (1.00)	0.527 (1.00)	0.431 (1.00)	0.0254 (1.00)	0.00431 (1.00)	0.816 (1.00)	0.00495 (1.00)	0.478 (1.00)	0.0245 (1.00)
1q loss	51 (5%)	1028	0.0735 (1.00)	0.0118 (1.00)	0.0004 (0.165)	0.211 (1.00)	0.337 (1.00)	0.176 (1.00)	0.0043 (1.00)	0.00219 (0.723)	0.0147 (1.00)	0.00113 (0.418)	0.0947 (1.00)	0.477 (1.00)
21q loss	180 (17%)	899	0.0345 (1.00)	0.151 (1.00)	1e-05 (0.0096)	0.0017 (0.586)	0.806 (1.00)	0.176 (1.00)	0.00125 (0.454)	0.00191 (0.638)	0.00859 (1.00)	0.0469 (1.00)	0.0197 (1.00)	0.0518 (1.00)
8q loss	93 (9%)	986	0.0514 (1.00)	0.104 (1.00)	0.00593 (1.00)	0.0191 (1.00)	0.801 (1.00)	0.337 (1.00)	0.00265 (0.856)	0.0945 (1.00)	0.387 (1.00)	0.856 (1.00)	0.22 (1.00)	0.385 (1.00)

'1p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
1P GAIN MUTATED	2	3	16	39	6	19	6	5
1P GAIN WILD-TYPE	19	33	103	57	103	53	14	35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
1P GAIN MUTATED	13	16	27	35	5
1P GAIN WILD-TYPE	88	136	87	53	53

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

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
1P GAIN MUTATED	36	48	8	103	10
1P GAIN WILD-TYPE	224	364	85	162	39

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
1P GAIN MUTATED	52	21	28	10	30
1P GAIN WILD-TYPE	80	176	149	78	98

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

'1p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
1P GAIN MUTATED	51	17	13
1P GAIN WILD-TYPE	98	115	104

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
1P GAIN MUTATED	4	12	30	25	10
1P GAIN WILD-TYPE	60	94	60	82	21

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
1P GAIN MUTATED	62	115	27
1P GAIN WILD-TYPE	481	183	205

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
1P GAIN MUTATED	26	33	38	11	77	19
1P GAIN WILD-TYPE	193	131	268	130	106	41

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
1P GAIN MUTATED	109	36	57
1P GAIN WILD-TYPE	222	217	419

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
1P GAIN MUTATED	42	48	36	12	7	57
1P GAIN WILD-TYPE	189	112	286	115	79	77

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
1P GAIN MUTATED	25	60	10	17	17
1P GAIN WILD-TYPE	155	79	89	94	116

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
1P GAIN MUTATED	80	37	12
1P GAIN WILD-TYPE	225	210	98

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
1Q GAIN MUTATED	172	242	89	172	31
1Q GAIN WILD-TYPE	88	170	4	93	18

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

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
ALL	219	164	306	141	183	60
1Q GAIN MUTATED	114	123	203	104	122	36
1Q GAIN WILD-TYPE	105	41	103	37	61	24

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.2

Table S15. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
1Q GAIN MUTATED	141	102	215	101	44	91
1Q GAIN WILD-TYPE	90	58	107	26	42	43

Figure S15. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S16. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
2P GAIN MUTATED	1	1	6	31	1	20	1	0
2P GAIN WILD-TYPE	20	35	113	65	108	52	19	40

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
2P GAIN MUTATED	5	1	27	27	1
2P GAIN WILD-TYPE	96	151	87	61	57

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
2P GAIN MUTATED	24	14	7	72	6
2P GAIN WILD-TYPE	236	398	86	193	43

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S19. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
2P GAIN MUTATED	38	2	19	6	13
2P GAIN WILD-TYPE	94	195	158	82	115

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S20. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
2P GAIN MUTATED	40	2	9
2P GAIN WILD-TYPE	109	130	108

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2P GAIN MUTATED	1	5	32	8	5
2P GAIN WILD-TYPE	63	101	58	99	26

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
2P GAIN MUTATED	29	93	1
2P GAIN WILD-TYPE	514	205	231

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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
ALL	219	164	306	141	183	60
2P GAIN MUTATED	8	27	6	2	57	23
2P GAIN WILD-TYPE	211	137	300	139	126	37

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

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S24. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
2P GAIN MUTATED	88	9	20
2P GAIN WILD-TYPE	243	244	456

Figure S24. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S25. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
2P GAIN MUTATED	27	40	6	3	1	40
2P GAIN WILD-TYPE	204	120	316	124	85	94

Figure S25. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S26. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
2P GAIN MUTATED	11	47	4	6	10
2P GAIN WILD-TYPE	169	92	95	105	123

Figure S26. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S27. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
2P GAIN MUTATED	53	20	5
2P GAIN WILD-TYPE	252	227	105

Figure S27. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S28. Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
2Q GAIN MUTATED	1	1	5	18	1	13	0	0
2Q GAIN WILD-TYPE	20	35	114	78	108	59	20	40

Figure S28. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
2Q GAIN MUTATED	4	1	17	16	1
2Q GAIN WILD-TYPE	97	151	97	72	57

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S30. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
2Q GAIN MUTATED	13	10	6	43	1
2Q GAIN WILD-TYPE	247	402	87	222	48

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
2Q GAIN MUTATED	22	1	12	3	4
2Q GAIN WILD-TYPE	110	196	165	85	124

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

'2q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S32. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
2Q GAIN MUTATED	26	2	4
2Q GAIN WILD-TYPE	123	130	113

Figure S32. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S33. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2Q GAIN MUTATED	1	3	19	5	4
2Q GAIN WILD-TYPE	63	103	71	102	27

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S34. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
2Q GAIN MUTATED	17	55	1
2Q GAIN WILD-TYPE	526	243	231

Figure S34. 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 = 0.0096

Table S35. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
2Q GAIN MUTATED	4	20	2	2	33	12
2Q GAIN WILD-TYPE	215	144	304	139	150	48

Figure S35. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S36. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
2Q GAIN MUTATED	48	7	13
2Q GAIN WILD-TYPE	283	246	463

Figure S36. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S37. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
2Q GAIN MUTATED	17	27	4	3	0	17
2Q GAIN WILD-TYPE	214	133	318	124	86	117

Figure S37. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S38. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
2Q GAIN MUTATED	6	29	2	6	6
2Q GAIN WILD-TYPE	174	110	97	105	127

Figure S38. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
3P GAIN MUTATED	46	13	20	46	10
3P GAIN WILD-TYPE	214	399	73	219	39

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S40. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
3P GAIN MUTATED	30	15	20	6	7
3P GAIN WILD-TYPE	102	182	157	82	121

Figure S40. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S41. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
3P GAIN MUTATED	78	49	7
3P GAIN WILD-TYPE	465	249	225

Figure S41. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S42. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
3P GAIN MUTATED	36	25	18	12	38	5
3P GAIN WILD-TYPE	183	139	288	129	145	55

Figure S42. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S43. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
3P GAIN MUTATED	28	24	18	21	11	29
3P GAIN WILD-TYPE	203	136	304	106	75	105

Figure S43. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.18

Table S44. Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
3Q GAIN MUTATED	2	7	29	32	16	17	7	1
3Q GAIN WILD-TYPE	19	29	90	64	93	55	13	39

Figure S44. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S45. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
3Q GAIN MUTATED	21	16	33	29	12
3Q GAIN WILD-TYPE	80	136	81	59	46

Figure S45. 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 = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
3Q GAIN MUTATED	59	23	25	94	11
3Q GAIN WILD-TYPE	201	389	68	171	38

Figure S46. 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 = 0.0096

Table S47. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
3Q GAIN MUTATED	52	19	34	10	11
3Q GAIN WILD-TYPE	80	178	143	78	117

Figure S47. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S48. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
3Q GAIN MUTATED	102	98	11
3Q GAIN WILD-TYPE	441	200	221

Figure S48. 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 = 0.0096

Table S49. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
3Q GAIN MUTATED	44	38	28	13	75	13
3Q GAIN WILD-TYPE	175	126	278	128	108	47

Figure S49. 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 = 0.0096

Table S50. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
3Q GAIN MUTATED	107	31	70
3Q GAIN WILD-TYPE	224	222	406

Figure S50. 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 = 0.0096

Table S51. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
3Q GAIN MUTATED	39	44	34	22	12	57
3Q GAIN WILD-TYPE	192	116	288	105	74	77

Figure S51. 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 = 0.0096

Table S52. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
3Q GAIN MUTATED	31	55	11	10	17
3Q GAIN WILD-TYPE	149	84	88	101	116

Figure S52. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S53. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
3Q GAIN MUTATED	78	33	13
3Q GAIN WILD-TYPE	227	214	97

Figure S53. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S54. Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4P GAIN MUTATED	1	2	22	3	3	4	0	2
4P GAIN WILD-TYPE	20	34	97	93	106	68	20	38

Figure S54. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S55. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
4P GAIN MUTATED	45	7	3	17	4
4P GAIN WILD-TYPE	215	405	90	248	45

Figure S55. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
4P GAIN MUTATED	31	17	15	3	7	3
4P GAIN WILD-TYPE	188	147	291	138	176	57

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

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.16

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
4P GAIN MUTATED	25	18	14	3	10	5
4P GAIN WILD-TYPE	206	142	308	124	76	129

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

'4q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S58. Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4Q GAIN MUTATED	1	2	23	2	3	2	0	2
4Q GAIN WILD-TYPE	20	34	96	94	106	70	20	38

Figure S58. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S59. Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
4Q GAIN MUTATED	18	8	6	2	1
4Q GAIN WILD-TYPE	83	144	108	86	57

Figure S59. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S60. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
4Q GAIN MUTATED	44	7	2	14	6
4Q GAIN WILD-TYPE	216	405	91	251	43

Figure S60. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S61. Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
4Q GAIN MUTATED	33	13	13	2	9	3
4Q GAIN WILD-TYPE	186	151	293	139	174	57

Figure S61. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S62. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
5P GAIN MUTATED	114	58	49	80	14
5P GAIN WILD-TYPE	146	354	44	185	35

Figure S62. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S63. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
5Q GAIN MUTATED	84	48	47	21	11
5Q GAIN WILD-TYPE	176	364	46	244	38

Figure S63. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.21

Table S64. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
5Q GAIN MUTATED	16	50	44	17	13
5Q GAIN WILD-TYPE	116	147	133	71	115

Figure S64. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.069

Table S65. Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
5Q GAIN MUTATED	22	23	5	24	7
5Q GAIN WILD-TYPE	42	83	85	83	24

Figure S65. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.24

Table S66. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
5Q GAIN MUTATED	125	37	48
5Q GAIN WILD-TYPE	418	261	184

Figure S66. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.089

Table S67. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
5Q GAIN MUTATED	56	40	57	33	17	7
5Q GAIN WILD-TYPE	163	124	249	108	166	53

Figure S67. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
5Q GAIN MUTATED	49	27	62	41	20	9
5Q GAIN WILD-TYPE	182	133	260	86	66	125

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

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.17

Table S69. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
5Q GAIN MUTATED	51	15	22	26	18
5Q GAIN WILD-TYPE	129	124	77	85	115

Figure S69. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S70. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6P GAIN MUTATED	2	2	18	36	13	19	7	2
6P GAIN WILD-TYPE	19	34	101	60	96	53	13	38

Figure S70. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S71. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
6P GAIN MUTATED	15	13	34	31	6
6P GAIN WILD-TYPE	86	139	80	57	52

Figure S71. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
6P GAIN MUTATED	43	20	20	114	10
6P GAIN WILD-TYPE	217	392	73	151	39

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

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
6P GAIN MUTATED	58	19	42	5	13
6P GAIN WILD-TYPE	74	178	135	83	115

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

'6p gain' versus 'RPPA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S74. Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
6P GAIN MUTATED	46	18	14
6P GAIN WILD-TYPE	103	114	103

Figure S74. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S75. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
6P GAIN MUTATED	85	108	13
6P GAIN WILD-TYPE	458	190	219

Figure S75. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S76. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
6P GAIN MUTATED	29	50	26	10	79	12
6P GAIN WILD-TYPE	190	114	280	131	104	48

Figure S76. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S77. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
6P GAIN MUTATED	116	24	59
6P GAIN WILD-TYPE	215	229	417

Figure S77. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S78. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
6P GAIN MUTATED	46	46	23	16	10	58
6P GAIN WILD-TYPE	185	114	299	111	76	76

Figure S78. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
6P GAIN MUTATED	22	61	13	8	17
6P GAIN WILD-TYPE	158	78	86	103	116

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S80. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
6P GAIN MUTATED	82	32	7
6P GAIN WILD-TYPE	223	215	103

Figure S80. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S81. Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6Q GAIN MUTATED	1	0	9	29	11	13	7	2
6Q GAIN WILD-TYPE	20	36	110	67	98	59	13	38

Figure S81. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S82. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
6Q GAIN MUTATED	9	11	24	24	4
6Q GAIN WILD-TYPE	92	141	90	64	54

Figure S82. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S83. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
6Q GAIN MUTATED	19	15	16	92	7
6Q GAIN WILD-TYPE	241	397	77	173	42

Figure S83. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S84. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
6Q GAIN MUTATED	43	9	29	3	11
6Q GAIN WILD-TYPE	89	188	148	85	117

Figure S84. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S85. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
6Q GAIN MUTATED	39	9	10
6Q GAIN WILD-TYPE	110	123	107

Figure S85. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S86. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
6Q GAIN MUTATED	54	83	11
6Q GAIN WILD-TYPE	489	215	221

Figure S86. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S87. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
6Q GAIN MUTATED	18	36	22	6	58	8
6Q GAIN WILD-TYPE	201	128	284	135	125	52

Figure S87. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S88. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
6Q GAIN MUTATED	92	17	34
6Q GAIN WILD-TYPE	239	236	442

Figure S88. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S89. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
6Q GAIN MUTATED	31	41	16	8	7	40
6Q GAIN WILD-TYPE	200	119	306	119	79	94

Figure S89. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S90. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
6Q GAIN MUTATED	17	48	11	6	12
6Q GAIN WILD-TYPE	163	91	88	105	121

Figure S90. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
6Q GAIN MUTATED	65	22	7
6Q GAIN WILD-TYPE	240	225	103

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

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S92. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
7P GAIN MUTATED	76	73	50	95	15
7P GAIN WILD-TYPE	184	339	43	170	34

Figure S92. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S93. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
7P GAIN MUTATED	52	51	60	23	17
7P GAIN WILD-TYPE	80	146	117	65	111

Figure S93. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
7P GAIN MUTATED	156	107	45
7P GAIN WILD-TYPE	387	191	187

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S95. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
7P GAIN MUTATED	62	64	59	35	61	27
7P GAIN WILD-TYPE	157	100	247	106	122	33

Figure S95. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S96. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
7Q GAIN MUTATED	63	58	45	88	12
7Q GAIN WILD-TYPE	197	354	48	177	37

Figure S96. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S97. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
7Q GAIN MUTATED	50	45	45	17	14
7Q GAIN WILD-TYPE	82	152	132	71	114

Figure S97. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
7Q GAIN MUTATED	123	103	39
7Q GAIN WILD-TYPE	420	195	193

Figure S98. 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 = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
7Q GAIN MUTATED	49	48	46	31	70	21
7Q GAIN WILD-TYPE	170	116	260	110	113	39

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S100. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
7Q GAIN MUTATED	45	43	68	37	12	54
7Q GAIN WILD-TYPE	186	117	254	90	74	80

Figure S100. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
8P GAIN MUTATED	69	81	37	77	25
8P GAIN WILD-TYPE	191	331	56	188	24

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

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S102. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
8P GAIN MUTATED	53	47	49	24	20
8P GAIN WILD-TYPE	79	150	128	64	108

Figure S102. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.21

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
8P GAIN MUTATED	156	92	40
8P GAIN WILD-TYPE	387	206	192

Figure S103. 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 = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
8P GAIN MUTATED	84	41	60	25	66	12
8P GAIN WILD-TYPE	135	123	246	116	117	48

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

'8q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
8Q GAIN MUTATED	14	12	74	62	43	35	15	14
8Q GAIN WILD-TYPE	7	24	45	34	66	37	5	26

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

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
8Q GAIN MUTATED	65	68	64	56	16
8Q GAIN WILD-TYPE	36	84	50	32	42

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

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
8Q GAIN MUTATED	152	122	40	170	44
8Q GAIN WILD-TYPE	108	290	53	95	5

Figure S107. 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 = 0.0096

Table S108. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
8Q GAIN MUTATED	91	75	91	31	54
8Q GAIN WILD-TYPE	41	122	86	57	74

Figure S108. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S109. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
8Q GAIN MUTATED	274	178	73
8Q GAIN WILD-TYPE	269	120	159

Figure S109. 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 = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
8Q GAIN MUTATED	142	93	112	27	121	30
8Q GAIN WILD-TYPE	77	71	194	114	62	30

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S111. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
8Q GAIN MUTATED	213	89	216
8Q GAIN WILD-TYPE	118	164	260

Figure S111. 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 = 0.0096

Table S112. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
8Q GAIN MUTATED	128	91	102	63	42	92
8Q GAIN WILD-TYPE	103	69	220	64	44	42

Figure S112. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S113. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
8Q GAIN MUTATED	94	99	35	35	51
8Q GAIN WILD-TYPE	86	40	64	76	82

Figure S113. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S114. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
8Q GAIN MUTATED	180	92	42
8Q GAIN WILD-TYPE	125	155	68

Figure S114. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S115. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9P GAIN MUTATED	1	2	3	34	14	9	0	5
9P GAIN WILD-TYPE	20	34	116	62	95	63	20	35

Figure S115. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S116. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
9P GAIN MUTATED	0	15	13	31	9
9P GAIN WILD-TYPE	101	137	101	57	49

Figure S116. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S117. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
9P GAIN MUTATED	13	25	29	66	8
9P GAIN WILD-TYPE	247	387	64	199	41

Figure S117. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S118. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
9P GAIN MUTATED	36	22	15	6	11
9P GAIN WILD-TYPE	96	175	162	82	117

Figure S118. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
9P GAIN MUTATED	9	9	26	4	6
9P GAIN WILD-TYPE	55	97	64	103	25

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

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
9P GAIN MUTATED	48	75	18
9P GAIN WILD-TYPE	495	223	214

Figure S120. 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 = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
9P GAIN MUTATED	19	22	22	14	58	6
9P GAIN WILD-TYPE	200	142	284	127	125	54

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

'9p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
9P GAIN MUTATED	72	22	43
9P GAIN WILD-TYPE	259	231	433

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

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
9P GAIN MUTATED	25	21	26	17	5	43
9P GAIN WILD-TYPE	206	139	296	110	81	91

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

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.19

Table S124. Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
9P GAIN MUTATED	24	34	9	13	9
9P GAIN WILD-TYPE	156	105	90	98	124

Figure S124. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S125. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
9Q GAIN MUTATED	18	24	29	42	6
9Q GAIN WILD-TYPE	242	388	64	223	43

Figure S125. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
10P GAIN MUTATED	2	4	17	42	11	27	6	4
10P GAIN WILD-TYPE	19	32	102	54	98	45	14	36

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

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S127. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
10P GAIN MUTATED	10	18	41	39	5
10P GAIN WILD-TYPE	91	134	73	49	53

Figure S127. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S128. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
10P GAIN MUTATED	47	28	15	116	8
10P GAIN WILD-TYPE	213	384	78	149	41

Figure S128. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S129. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
10P GAIN MUTATED	59	13	34	5	22
10P GAIN WILD-TYPE	73	184	143	83	106

Figure S129. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S130. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
10P GAIN MUTATED	53	17	20
10P GAIN WILD-TYPE	96	115	97

Figure S130. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S131. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
10P GAIN MUTATED	7	18	40	19	6
10P GAIN WILD-TYPE	57	88	50	88	25

Figure S131. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S132. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
10P GAIN MUTATED	79	118	17
10P GAIN WILD-TYPE	464	180	215

Figure S132. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S133. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
10P GAIN MUTATED	33	42	33	4	81	21
10P GAIN WILD-TYPE	186	122	273	137	102	39

Figure S133. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S134. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
10P GAIN MUTATED	122	26	62
10P GAIN WILD-TYPE	209	227	414

Figure S134. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S135. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
10P GAIN MUTATED	50	54	24	18	7	57
10P GAIN WILD-TYPE	181	106	298	109	79	77

Figure S135. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S136. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
10P GAIN MUTATED	29	62	11	10	16
10P GAIN WILD-TYPE	151	77	88	101	117

Figure S136. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S137. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
10P GAIN MUTATED	89	26	13
10P GAIN WILD-TYPE	216	221	97

Figure S137. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S138. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
10Q GAIN MUTATED	29	21	13	56	5
10Q GAIN WILD-TYPE	231	391	80	209	44

Figure S138. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S139. Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
10Q GAIN MUTATED	57	57	10
10Q GAIN WILD-TYPE	486	241	222

Figure S139. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S140. Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
10Q GAIN MUTATED	24	28	23	3	32	14
10Q GAIN WILD-TYPE	195	136	283	138	151	46

Figure S140. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S141. Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
10Q GAIN MUTATED	65	16	41
10Q GAIN WILD-TYPE	266	237	435

Figure S141. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S142. Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
10Q GAIN MUTATED	31	30	17	15	4	25
10Q GAIN WILD-TYPE	200	130	305	112	82	109

Figure S142. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S143. Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
10Q GAIN MUTATED	21	30	5	7	9
10Q GAIN WILD-TYPE	159	109	94	104	124

Figure S143. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S144. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
11P GAIN MUTATED	46	18	14	53	6
11P GAIN WILD-TYPE	214	394	79	212	43

Figure S144. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S145. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
11P GAIN MUTATED	67	54	16
11P GAIN WILD-TYPE	476	244	216

Figure S145. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S146. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
11P GAIN MUTATED	58	14	63
11P GAIN WILD-TYPE	273	239	413

Figure S146. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.12

Table S147. Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
11P GAIN MUTATED	53	15	15
11P GAIN WILD-TYPE	252	232	95

Figure S147. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S148. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
11Q GAIN MUTATED	20	11	11	46	6
11Q GAIN WILD-TYPE	240	401	82	219	43

Figure S148. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.22

Table S149. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
11Q GAIN MUTATED	25	16	10	5	6
11Q GAIN WILD-TYPE	107	181	167	83	122

Figure S149. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S150. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
11Q GAIN MUTATED	38	47	9
11Q GAIN WILD-TYPE	505	251	223

Figure S150. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S151. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
11Q GAIN MUTATED	13	19	17	7	27	11
11Q GAIN WILD-TYPE	206	145	289	134	156	49

Figure S151. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S152. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
11Q GAIN MUTATED	48	10	33
11Q GAIN WILD-TYPE	283	243	443

Figure S152. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S153. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
11Q GAIN MUTATED	14	25	17	8	7	20
11Q GAIN WILD-TYPE	217	135	305	119	79	114

Figure S153. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S154. Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
12P GAIN MUTATED	27	16	33	29	9
12P GAIN WILD-TYPE	74	136	81	59	49

Figure S154. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S155. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
12P GAIN MUTATED	87	21	24	84	11
12P GAIN WILD-TYPE	173	391	69	181	38

Figure S155. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S156. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
12P GAIN MUTATED	124	83	20
12P GAIN WILD-TYPE	419	215	212

Figure S156. 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 = 0.0096

Table S157. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
12P GAIN MUTATED	56	51	38	12	57	13
12P GAIN WILD-TYPE	163	113	268	129	126	47

Figure S157. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S158. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
12P GAIN MUTATED	101	35	84
12P GAIN WILD-TYPE	230	218	392

Figure S158. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.069

Table S159. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
12P GAIN MUTATED	56	37	45	26	12	44
12P GAIN WILD-TYPE	175	123	277	101	74	90

Figure S159. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S160. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
12Q GAIN MUTATED	93	20	25	42	10
12Q GAIN WILD-TYPE	167	392	68	223	39

Figure S160. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S161. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
12Q GAIN MUTATED	127	44	18
12Q GAIN WILD-TYPE	416	254	214

Figure S161. 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 = 0.0096

Table S162. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
12Q GAIN MUTATED	56	50	35	17	22	9
12Q GAIN WILD-TYPE	163	114	271	124	161	51

Figure S162. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S163. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
13Q GAIN MUTATED	23	14	9	41	5
13Q GAIN WILD-TYPE	237	398	84	224	44

Figure S163. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
13Q GAIN MUTATED	47	39	6
13Q GAIN WILD-TYPE	496	259	226

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

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
13Q GAIN MUTATED	21	17	9	11	23	11
13Q GAIN WILD-TYPE	198	147	297	130	160	49

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

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.12

Table S166. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
13Q GAIN MUTATED	46	15	29
13Q GAIN WILD-TYPE	285	238	447

Figure S166. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.18

Table S167. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
13Q GAIN MUTATED	19	27	13	11	6	14
13Q GAIN WILD-TYPE	212	133	309	116	80	120

Figure S167. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S168. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
14Q GAIN MUTATED	58	29	19	30	7
14Q GAIN WILD-TYPE	202	383	74	235	42

Figure S168. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S169. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
14Q GAIN MUTATED	95	32	15
14Q GAIN WILD-TYPE	448	266	217

Figure S169. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S170. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
14Q GAIN MUTATED	40	34	26	17	12	13
14Q GAIN WILD-TYPE	179	130	280	124	171	47

Figure S170. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S171. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
14Q GAIN MUTATED	45	33	27	27	6	4
14Q GAIN WILD-TYPE	186	127	295	100	80	130

Figure S171. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.069

Table S172. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
15Q GAIN MUTATED	30	19	4	33	1
15Q GAIN WILD-TYPE	230	393	89	232	48

Figure S172. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S173. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16P GAIN MUTATED	11	14	52	33	73	36	12	14
16P GAIN WILD-TYPE	10	22	67	63	36	36	8	26

Figure S173. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S174. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
16P GAIN MUTATED	124	156	64	98	21
16P GAIN WILD-TYPE	136	256	29	167	28

Figure S174. 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 = 0.0096

Table S175. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
16P GAIN MUTATED	44	100	86	31	31
16P GAIN WILD-TYPE	88	97	91	57	97

Figure S175. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S176. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
16P GAIN MUTATED	48	54	31	45	11
16P GAIN WILD-TYPE	16	52	59	62	20

Figure S176. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S177. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
16P GAIN MUTATED	270	96	95
16P GAIN WILD-TYPE	273	202	137

Figure S177. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S178. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
16P GAIN MUTATED	111	81	126	70	47	26
16P GAIN WILD-TYPE	108	83	180	71	136	34

Figure S178. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S179. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
16P GAIN MUTATED	115	96	241
16P GAIN WILD-TYPE	216	157	235

Figure S179. 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 = 0.0096

Table S180. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
16P GAIN MUTATED	97	76	127	78	44	30
16P GAIN WILD-TYPE	134	84	195	49	42	104

Figure S180. 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 = 0.0096

Table S181. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
16P GAIN MUTATED	96	35	47	45	50
16P GAIN WILD-TYPE	84	104	52	66	83

Figure S181. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.073

Table S182. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
16Q GAIN MUTATED	26	41	33	11	12	15
16Q GAIN WILD-TYPE	205	119	289	116	74	119

Figure S182. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S183. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
17P GAIN MUTATED	49	19	10	21	7
17P GAIN WILD-TYPE	211	393	83	244	42

Figure S183. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S184. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q GAIN MUTATED	3	8	46	8	10	11	5	4
17Q GAIN WILD-TYPE	18	28	73	88	99	61	15	36

Figure S184. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S185. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
17Q GAIN MUTATED	34	23	24	7	7
17Q GAIN WILD-TYPE	67	129	90	81	51

Figure S185. 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 = 0.0096

Table S186. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
17Q GAIN MUTATED	115	35	14	37	15
17Q GAIN WILD-TYPE	145	377	79	228	34

Figure S186. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.057

Table S187. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
17Q GAIN MUTATED	17	41	60	15	21
17Q GAIN WILD-TYPE	115	156	117	73	107

Figure S187. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.061

Table S188. Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
17Q GAIN MUTATED	6	21	8	36	4
17Q GAIN WILD-TYPE	58	85	82	71	27

Figure S188. 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 = 0.0096

Table S189. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
17Q GAIN MUTATED	145	41	29
17Q GAIN WILD-TYPE	398	257	203

Figure S189. 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 = 0.0096

Table S190. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
17Q GAIN MUTATED	88	40	42	18	19	8
17Q GAIN WILD-TYPE	131	124	264	123	164	52

Figure S190. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.1

Table S191. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
17Q GAIN MUTATED	64	31	56	22	25	13
17Q GAIN WILD-TYPE	167	129	266	105	61	121

Figure S191. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S192. Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18P GAIN MUTATED	1	1	19	35	16	10	4	1
18P GAIN WILD-TYPE	20	35	100	61	93	62	16	39

Figure S192. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S193. Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18P GAIN MUTATED	20	13	17	32	5
18P GAIN WILD-TYPE	81	139	97	56	53

Figure S193. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S194. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
18P GAIN MUTATED	41	23	19	82	12
18P GAIN WILD-TYPE	219	389	74	183	37

Figure S194. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S195. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18P GAIN MUTATED	52	22	15	6	13
18P GAIN WILD-TYPE	80	175	162	82	115

Figure S195. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S196. Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
18P GAIN MUTATED	13	9	34	10	4
18P GAIN WILD-TYPE	51	97	56	97	27

Figure S196. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S197. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
18P GAIN MUTATED	84	86	7
18P GAIN WILD-TYPE	459	212	225

Figure S197. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S198. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
18P GAIN MUTATED	43	21	13	16	70	14
18P GAIN WILD-TYPE	176	143	293	125	113	46

Figure S198. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S199. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
18P GAIN MUTATED	97	22	51
18P GAIN WILD-TYPE	234	231	425

Figure S199. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S200. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
18P GAIN MUTATED	24	37	23	19	13	54
18P GAIN WILD-TYPE	207	123	299	108	73	80

Figure S200. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S201. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
18P GAIN MUTATED	26	51	10	11	11
18P GAIN WILD-TYPE	154	88	89	100	122

Figure S201. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S202. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
18P GAIN MUTATED	72	21	16
18P GAIN WILD-TYPE	233	226	94

Figure S202. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S203. Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18Q GAIN MUTATED	2	1	21	30	17	5	4	1
18Q GAIN WILD-TYPE	19	35	98	66	92	67	16	39

Figure S203. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S204. Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18Q GAIN MUTATED	22	13	14	27	5
18Q GAIN WILD-TYPE	79	139	100	61	53

Figure S204. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S205. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
18Q GAIN MUTATED	37	17	20	67	12
18Q GAIN WILD-TYPE	223	395	73	198	37

Figure S205. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S206. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18Q GAIN MUTATED	34	24	15	6	11
18Q GAIN WILD-TYPE	98	173	162	82	117

Figure S206. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S207. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
18Q GAIN MUTATED	83	62	8
18Q GAIN WILD-TYPE	460	236	224

Figure S207. 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 = 0.0096

Table S208. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
18Q GAIN MUTATED	46	17	16	15	53	6
18Q GAIN WILD-TYPE	173	147	290	126	130	54

Figure S208. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S209. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
18Q GAIN MUTATED	76	19	52
18Q GAIN WILD-TYPE	255	234	424

Figure S209. 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 = 0.0096

Table S210. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
18Q GAIN MUTATED	27	24	23	20	13	40
18Q GAIN WILD-TYPE	204	136	299	107	73	94

Figure S210. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.11

Table S211. Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19P GAIN MUTATED	6	3	15	29	15	11	9	4
19P GAIN WILD-TYPE	15	33	104	67	94	61	11	36

Figure S211. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S212. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
19P GAIN MUTATED	38	36	29	78	8
19P GAIN WILD-TYPE	222	376	64	187	41

Figure S212. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S213. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
19P GAIN MUTATED	77	81	30
19P GAIN WILD-TYPE	466	217	202

Figure S213. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S214. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
19P GAIN MUTATED	31	27	44	15	55	16
19P GAIN WILD-TYPE	188	137	262	126	128	44

Figure S214. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S215. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
19P GAIN MUTATED	86	40	60
19P GAIN WILD-TYPE	245	213	416

Figure S215. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S216. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
19P GAIN MUTATED	38	40	41	18	10	39
19P GAIN WILD-TYPE	193	120	281	109	76	95

Figure S216. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S217. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
19Q GAIN MUTATED	48	40	31	90	13
19Q GAIN WILD-TYPE	212	372	62	175	36

Figure S217. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S218. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
19Q GAIN MUTATED	94	91	36
19Q GAIN WILD-TYPE	449	207	196

Figure S218. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S219. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
19Q GAIN MUTATED	42	34	49	15	62	19
19Q GAIN WILD-TYPE	177	130	257	126	121	41

Figure S219. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S220. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
19Q GAIN MUTATED	102	43	75
19Q GAIN WILD-TYPE	229	210	401

Figure S220. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S221. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
19Q GAIN MUTATED	49	52	49	19	11	40
19Q GAIN WILD-TYPE	182	108	273	108	75	94

Figure S221. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S222. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20P GAIN MUTATED	8	13	49	42	34	42	15	7
20P GAIN WILD-TYPE	13	23	70	54	75	30	5	33

Figure S222. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S223. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
20P GAIN MUTATED	42	45	68	38	17
20P GAIN WILD-TYPE	59	107	46	50	41

Figure S223. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S224. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
20P GAIN MUTATED	146	59	56	132	22
20P GAIN WILD-TYPE	114	353	37	133	27

Figure S224. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S225. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
20P GAIN MUTATED	229	131	53
20P GAIN WILD-TYPE	314	167	179

Figure S225. 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 = 0.0096

Table S226. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
20P GAIN MUTATED	103	91	86	33	77	23
20P GAIN WILD-TYPE	116	73	220	108	106	37

Figure S226. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S227. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
20P GAIN MUTATED	160	65	184
20P GAIN WILD-TYPE	171	188	292

Figure S227. 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 = 0.0096

Table S228. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
20P GAIN MUTATED	102	81	83	61	27	55
20P GAIN WILD-TYPE	129	79	239	66	59	79

Figure S228. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S229. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
20P GAIN MUTATED	90	68	32	37	35
20P GAIN WILD-TYPE	90	71	67	74	98

Figure S229. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S230. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20Q GAIN MUTATED	7	13	61	40	35	42	15	10
20Q GAIN WILD-TYPE	14	23	58	56	74	30	5	30

Figure S230. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S231. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
20Q GAIN MUTATED	52	49	71	34	17
20Q GAIN WILD-TYPE	49	103	43	54	41

Figure S231. 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 = 0.0096

Table S232. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
20Q GAIN MUTATED	170	62	55	139	24
20Q GAIN WILD-TYPE	90	350	38	126	25

Figure S232. 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 = 0.0096

Table S233. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
20Q GAIN MUTATED	62	71	98	25	40
20Q GAIN WILD-TYPE	70	126	79	63	88

Figure S233. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S234. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
20Q GAIN MUTATED	257	136	55
20Q GAIN WILD-TYPE	286	162	177

Figure S234. 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 = 0.0096

Table S235. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
20Q GAIN MUTATED	123	96	91	34	78	26
20Q GAIN WILD-TYPE	96	68	215	107	105	34

Figure S235. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S236. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
20Q GAIN MUTATED	171	69	205
20Q GAIN WILD-TYPE	160	184	271

Figure S236. 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 = 0.0096

Table S237. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
20Q GAIN MUTATED	127	82	88	59	31	58
20Q GAIN WILD-TYPE	104	78	234	68	55	76

Figure S237. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S238. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
20Q GAIN MUTATED	103	72	37	40	39
20Q GAIN WILD-TYPE	77	67	62	71	94

Figure S238. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S239. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
20Q GAIN MUTATED	158	84	49
20Q GAIN WILD-TYPE	147	163	61

Figure S239. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S240. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
21Q GAIN MUTATED	2	2	16	31	11	31	8	3
21Q GAIN WILD-TYPE	19	34	103	65	98	41	12	37

Figure S240. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S241. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
21Q GAIN MUTATED	12	15	44	27	6
21Q GAIN WILD-TYPE	89	137	70	61	52

Figure S241. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S242. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
21Q GAIN MUTATED	39	30	22	92	12
21Q GAIN WILD-TYPE	221	382	71	173	37

Figure S242. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S243. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
21Q GAIN MUTATED	47	16	33	10	15
21Q GAIN WILD-TYPE	85	181	144	78	113

Figure S243. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S244. Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
21Q GAIN MUTATED	47	16	22
21Q GAIN WILD-TYPE	102	116	95

Figure S244. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S245. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
21Q GAIN MUTATED	77	104	14
21Q GAIN WILD-TYPE	466	194	218

Figure S245. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S246. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
21Q GAIN MUTATED	36	43	21	10	61	24
21Q GAIN WILD-TYPE	183	121	285	131	122	36

Figure S246. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S247. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
21Q GAIN MUTATED	101	28	61
21Q GAIN WILD-TYPE	230	225	415

Figure S247. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S248. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
21Q GAIN MUTATED	40	51	29	18	8	44
21Q GAIN WILD-TYPE	191	109	293	109	78	90

Figure S248. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S249. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
21Q GAIN MUTATED	29	51	6	12	19
21Q GAIN WILD-TYPE	151	88	93	99	114

Figure S249. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S250. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
21Q GAIN MUTATED	78	30	9
21Q GAIN WILD-TYPE	227	217	101

Figure S250. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S251. Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
22Q GAIN MUTATED	3	0	12	18	2	15	2	0
22Q GAIN WILD-TYPE	18	36	107	78	107	57	18	40

Figure S251. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S252. Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
22Q GAIN MUTATED	9	3	24	15	1
22Q GAIN WILD-TYPE	92	149	90	73	57

Figure S252. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S253. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
22Q GAIN MUTATED	25	9	3	55	6
22Q GAIN WILD-TYPE	235	403	90	210	43

Figure S253. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S254. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
22Q GAIN MUTATED	22	8	19	3	9
22Q GAIN WILD-TYPE	110	189	158	85	119

Figure S254. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S255. Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
22Q GAIN MUTATED	31	5	8
22Q GAIN WILD-TYPE	118	127	109

Figure S255. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S256. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
22Q GAIN MUTATED	36	60	1
22Q GAIN WILD-TYPE	507	238	231

Figure S256. 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 = 0.0096

Table S257. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
22Q GAIN MUTATED	19	24	7	2	33	12
22Q GAIN WILD-TYPE	200	140	299	139	150	48

Figure S257. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S258. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
22Q GAIN MUTATED	55	7	33
22Q GAIN WILD-TYPE	276	246	443

Figure S258. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S259. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
22Q GAIN MUTATED	26	28	10	3	6	22
22Q GAIN WILD-TYPE	205	132	312	124	80	112

Figure S259. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S260. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
22Q GAIN MUTATED	13	25	6	4	6
22Q GAIN WILD-TYPE	167	114	93	107	127

Figure S260. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S261. Gene #40: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
XQ GAIN MUTATED	2	1	17	25	13	19	4	1
XQ GAIN WILD-TYPE	19	35	102	71	96	53	16	39

Figure S261. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S262. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
XQ GAIN MUTATED	37	15	22	57	9
XQ GAIN WILD-TYPE	223	397	71	208	40

Figure S262. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S263. Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
XQ GAIN MUTATED	27	19	22	4	3
XQ GAIN WILD-TYPE	105	178	155	84	125

Figure S263. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S264. Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
XQ GAIN MUTATED	72	58	9
XQ GAIN WILD-TYPE	471	240	223

Figure S264. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S265. Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
XQ GAIN MUTATED	31	27	14	15	44	8
XQ GAIN WILD-TYPE	188	137	292	126	139	52

Figure S265. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S266. Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
XQ GAIN MUTATED	73	9	51
XQ GAIN WILD-TYPE	258	244	425

Figure S266. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S267. Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
XQ GAIN MUTATED	31	25	13	17	14	33
XQ GAIN WILD-TYPE	200	135	309	110	72	101

Figure S267. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S268. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
1P LOSS MUTATED	33	23	42	10	14
1P LOSS WILD-TYPE	68	129	72	78	44

Figure S268. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S269. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
1P LOSS MUTATED	96	37	47	49	14
1P LOSS WILD-TYPE	164	375	46	216	35

Figure S269. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S270. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
1P LOSS MUTATED	21	40	63	12	17
1P LOSS WILD-TYPE	111	157	114	76	111

Figure S270. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S271. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
1P LOSS MUTATED	166	47	28
1P LOSS WILD-TYPE	377	251	204

Figure S271. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S272. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
1P LOSS MUTATED	67	67	51	25	22	9
1P LOSS WILD-TYPE	152	97	255	116	161	51

Figure S272. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S273. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
1P LOSS MUTATED	65	34	51	48	24	16
1P LOSS WILD-TYPE	166	126	271	79	62	118

Figure S273. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.16

Table S274. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
1Q LOSS MUTATED	19	6	4	18	4
1Q LOSS WILD-TYPE	241	406	89	247	45

Figure S274. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S275. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
2P LOSS MUTATED	76	30	26	36	13
2P LOSS WILD-TYPE	184	382	67	229	36

Figure S275. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.19

Table S276. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
2P LOSS MUTATED	14	43	37	9	10
2P LOSS WILD-TYPE	118	154	140	79	118

Figure S276. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.22

Table S277. Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2P LOSS MUTATED	18	11	8	29	6
2P LOSS WILD-TYPE	46	95	82	78	25

Figure S277. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S278. Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
2P LOSS MUTATED	130	27	22
2P LOSS WILD-TYPE	413	271	210

Figure S278. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S279. Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
2P LOSS MUTATED	63	42	36	20	16	2
2P LOSS WILD-TYPE	156	122	270	121	167	58

Figure S279. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S280. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
2P LOSS MUTATED	46	26	105
2P LOSS WILD-TYPE	285	227	371

Figure S280. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S281. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
2P LOSS MUTATED	51	20	42	30	21	13
2P LOSS WILD-TYPE	180	140	280	97	65	121

Figure S281. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S282. Gene #43: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
2P LOSS MUTATED	49	10	10	16	15
2P LOSS WILD-TYPE	131	129	89	95	118

Figure S282. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S283. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
2Q LOSS MUTATED	82	33	28	51	16
2Q LOSS WILD-TYPE	178	379	65	214	33

Figure S283. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S284. Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
2Q LOSS MUTATED	132	52	24
2Q LOSS WILD-TYPE	411	246	208

Figure S284. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S285. Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
2Q LOSS MUTATED	64	46	41	20	33	4
2Q LOSS WILD-TYPE	155	118	265	121	150	56

Figure S285. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.24

Table S286. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
2Q LOSS MUTATED	69	29	108
2Q LOSS WILD-TYPE	262	224	368

Figure S286. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.12

Table S287. Gene #44: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
2Q LOSS MUTATED	53	22	11	18	16
2Q LOSS WILD-TYPE	127	117	88	93	117

Figure S287. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S288. Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
3P LOSS MUTATED	0	7	19	29	4	17	6	4
3P LOSS WILD-TYPE	21	29	100	67	105	55	14	36

Figure S288. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S289. Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
3P LOSS MUTATED	15	18	27	26	0
3P LOSS WILD-TYPE	86	134	87	62	58

Figure S289. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S290. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
3P LOSS MUTATED	54	28	13	86	5
3P LOSS WILD-TYPE	206	384	80	179	44

Figure S290. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S291. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
3P LOSS MUTATED	38	15	45	9	17
3P LOSS WILD-TYPE	94	182	132	79	111

Figure S291. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S292. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
3P LOSS MUTATED	2	14	31	19	7
3P LOSS WILD-TYPE	62	92	59	88	24

Figure S292. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S293. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
3P LOSS MUTATED	76	89	20
3P LOSS WILD-TYPE	467	209	212

Figure S293. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S294. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
3P LOSS MUTATED	33	43	35	4	55	15
3P LOSS WILD-TYPE	186	121	271	137	128	45

Figure S294. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S295. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
3P LOSS MUTATED	99	29	52
3P LOSS WILD-TYPE	232	224	424

Figure S295. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S296. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
3P LOSS MUTATED	50	41	35	9	6	39
3P LOSS WILD-TYPE	181	119	287	118	80	95

Figure S296. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S297. Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
3P LOSS MUTATED	27	48	9	9	24
3P LOSS WILD-TYPE	153	91	90	102	109

Figure S297. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.1

Table S298. Gene #46: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
3Q LOSS MUTATED	10	7	19	12	0
3Q LOSS WILD-TYPE	91	145	95	76	58

Figure S298. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S299. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
3Q LOSS MUTATED	33	13	9	44	4
3Q LOSS WILD-TYPE	227	399	84	221	45

Figure S299. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S300. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
3Q LOSS MUTATED	22	28	16	4	24	9
3Q LOSS WILD-TYPE	197	136	290	137	159	51

Figure S300. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S301. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
3Q LOSS MUTATED	52	16	31
3Q LOSS WILD-TYPE	279	237	445

Figure S301. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S302. Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
3Q LOSS MUTATED	34	21	17	5	5	17
3Q LOSS WILD-TYPE	197	139	305	122	81	117

Figure S302. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S303. Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4P LOSS MUTATED	4	7	25	60	22	41	8	7
4P LOSS WILD-TYPE	17	29	94	36	87	31	12	33

Figure S303. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S304. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
4P LOSS MUTATED	24	28	57	54	11
4P LOSS WILD-TYPE	77	124	57	34	47

Figure S304. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S305. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
4P LOSS MUTATED	77	53	45	164	14
4P LOSS WILD-TYPE	183	359	48	101	35

Figure S305. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S306. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
4P LOSS MUTATED	90	38	53	15	28
4P LOSS WILD-TYPE	42	159	124	73	100

Figure S306. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S307. Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
4P LOSS MUTATED	77	39	25
4P LOSS WILD-TYPE	72	93	92

Figure S307. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S308. Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
4P LOSS MUTATED	18	28	53	29	13
4P LOSS WILD-TYPE	46	78	37	78	18

Figure S308. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S309. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
4P LOSS MUTATED	141	180	30
4P LOSS WILD-TYPE	402	118	202

Figure S309. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S310. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
4P LOSS MUTATED	52	70	53	24	120	32
4P LOSS WILD-TYPE	167	94	253	117	63	28

Figure S310. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S311. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
4P LOSS MUTATED	178	47	117
4P LOSS WILD-TYPE	153	206	359

Figure S311. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S312. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
4P LOSS MUTATED	69	74	52	40	18	89
4P LOSS WILD-TYPE	162	86	270	87	68	45

Figure S312. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S313. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
4P LOSS MUTATED	49	93	19	27	25
4P LOSS WILD-TYPE	131	46	80	84	108

Figure S313. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S314. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
4P LOSS MUTATED	124	56	33
4P LOSS WILD-TYPE	181	191	77

Figure S314. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S315. Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
4Q LOSS MUTATED	4	7	24	46	21	36	7	7
4Q LOSS WILD-TYPE	17	29	95	50	88	36	13	33

Figure S315. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S316. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
4Q LOSS MUTATED	24	26	50	41	11
4Q LOSS WILD-TYPE	77	126	64	47	47

Figure S316. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S317. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
4Q LOSS MUTATED	69	50	45	136	12
4Q LOSS WILD-TYPE	191	362	48	129	37

Figure S317. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S318. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
4Q LOSS MUTATED	72	40	46	15	28
4Q LOSS WILD-TYPE	60	157	131	73	100

Figure S318. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S319. Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
4Q LOSS MUTATED	64	35	25
4Q LOSS WILD-TYPE	85	97	92

Figure S319. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S320. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
4Q LOSS MUTATED	137	147	26
4Q LOSS WILD-TYPE	406	151	206

Figure S320. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S321. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
4Q LOSS MUTATED	47	67	51	24	94	27
4Q LOSS WILD-TYPE	172	97	255	117	89	33

Figure S321. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S322. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
4Q LOSS MUTATED	142	45	114
4Q LOSS WILD-TYPE	189	208	362

Figure S322. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S323. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
4Q LOSS MUTATED	63	63	50	39	18	68
4Q LOSS WILD-TYPE	168	97	272	88	68	66

Figure S323. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S324. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
4Q LOSS MUTATED	46	69	19	27	21
4Q LOSS WILD-TYPE	134	70	80	84	112

Figure S324. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S325. Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
5P LOSS MUTATED	1	1	8	40	5	11	1	2
5P LOSS WILD-TYPE	20	35	111	56	104	61	19	38

Figure S325. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S326. Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
5P LOSS MUTATED	9	5	17	37	1
5P LOSS WILD-TYPE	92	147	97	51	57

Figure S326. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S327. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
5P LOSS MUTATED	18	13	4	97	8
5P LOSS WILD-TYPE	242	399	89	168	41

Figure S327. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S328. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
5P LOSS MUTATED	51	8	13	4	17
5P LOSS WILD-TYPE	81	189	164	84	111

Figure S328. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S329. Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
5P LOSS MUTATED	43	9	9
5P LOSS WILD-TYPE	106	123	108

Figure S329. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S330. Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
5P LOSS MUTATED	1	7	38	12	3
5P LOSS WILD-TYPE	63	99	52	95	28

Figure S330. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S331. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
5P LOSS MUTATED	40	94	5
5P LOSS WILD-TYPE	503	204	227

Figure S331. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S332. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
5P LOSS MUTATED	15	25	12	1	78	8
5P LOSS WILD-TYPE	204	139	294	140	105	52

Figure S332. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S333. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
5P LOSS MUTATED	97	15	25
5P LOSS WILD-TYPE	234	238	451

Figure S333. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S334. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
5P LOSS MUTATED	28	30	10	3	5	61
5P LOSS WILD-TYPE	203	130	312	124	81	73

Figure S334. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S335. Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
5P LOSS MUTATED	12	56	5	4	9
5P LOSS WILD-TYPE	168	83	94	107	124

Figure S335. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S336. Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
5P LOSS MUTATED	70	12	4
5P LOSS WILD-TYPE	235	235	106

Figure S336. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S337. Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
5Q LOSS MUTATED	2	3	14	60	4	21	5	3
5Q LOSS WILD-TYPE	19	33	105	36	105	51	15	37

Figure S337. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S338. Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
5Q LOSS MUTATED	14	10	32	55	1
5Q LOSS WILD-TYPE	87	142	82	33	57

Figure S338. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S339. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
5Q LOSS MUTATED	29	19	5	164	11
5Q LOSS WILD-TYPE	231	393	88	101	38

Figure S339. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S340. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
5Q LOSS MUTATED	86	8	21	7	29
5Q LOSS WILD-TYPE	46	189	156	81	99

Figure S340. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S341. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
5Q LOSS MUTATED	68	10	18
5Q LOSS WILD-TYPE	81	122	99

Figure S341. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S342. Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
5Q LOSS MUTATED	3	14	55	18	6
5Q LOSS WILD-TYPE	61	92	35	89	25

Figure S342. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S343. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
5Q LOSS MUTATED	61	156	10
5Q LOSS WILD-TYPE	482	142	222

Figure S343. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S344. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
5Q LOSS MUTATED	24	38	24	2	119	20
5Q LOSS WILD-TYPE	195	126	282	139	64	40

Figure S344. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S345. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
5Q LOSS MUTATED	162	23	38
5Q LOSS WILD-TYPE	169	230	438

Figure S345. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S346. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
5Q LOSS MUTATED	44	58	15	6	6	94
5Q LOSS WILD-TYPE	187	102	307	121	80	40

Figure S346. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S347. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
5Q LOSS MUTATED	16	88	13	9	14
5Q LOSS WILD-TYPE	164	51	86	102	119

Figure S347. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S348. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
5Q LOSS MUTATED	107	25	8
5Q LOSS WILD-TYPE	198	222	102

Figure S348. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S349. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
6P LOSS MUTATED	82	45	17	32	12
6P LOSS WILD-TYPE	178	367	76	233	37

Figure S349. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S350. Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
6P LOSS MUTATED	119	36	31
6P LOSS WILD-TYPE	424	262	201

Figure S350. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S351. Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
6Q LOSS MUTATED	6	13	44	13	23	14	1	14
6Q LOSS WILD-TYPE	15	23	75	83	86	58	19	26

Figure S351. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S352. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
6Q LOSS MUTATED	117	77	23	41	18
6Q LOSS WILD-TYPE	143	335	70	224	31

Figure S352. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.12

Table S353. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
6Q LOSS MUTATED	164	52	58
6Q LOSS WILD-TYPE	379	246	174

Figure S353. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S354. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
6Q LOSS MUTATED	78	43	79	32	26	16
6Q LOSS WILD-TYPE	141	121	227	109	157	44

Figure S354. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S355. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
7P LOSS MUTATED	40	10	6	52	3
7P LOSS WILD-TYPE	220	402	87	213	46

Figure S355. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S356. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
7P LOSS MUTATED	55	49	6
7P LOSS WILD-TYPE	488	249	226

Figure S356. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S357. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
7P LOSS MUTATED	27	25	15	7	31	5
7P LOSS WILD-TYPE	192	139	291	134	152	55

Figure S357. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S358. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
7P LOSS MUTATED	61	6	42
7P LOSS WILD-TYPE	270	247	434

Figure S358. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S359. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
7P LOSS MUTATED	32	22	8	12	9	26
7P LOSS WILD-TYPE	199	138	314	115	77	108

Figure S359. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.073

Table S360. Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
7P LOSS MUTATED	44	13	5
7P LOSS WILD-TYPE	261	234	105

Figure S360. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S361. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
7Q LOSS MUTATED	44	21	10	41	3
7Q LOSS WILD-TYPE	216	391	83	224	46

Figure S361. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.089

Table S362. Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
7Q LOSS MUTATED	74	34	10
7Q LOSS WILD-TYPE	469	264	222

Figure S362. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S363. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
7Q LOSS MUTATED	54	8	55
7Q LOSS WILD-TYPE	277	245	421

Figure S363. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S364. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
7Q LOSS MUTATED	37	26	13	17	11	13
7Q LOSS WILD-TYPE	194	134	309	110	75	121

Figure S364. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S365. Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
8P LOSS MUTATED	5	10	56	45	22	37	11	17
8P LOSS WILD-TYPE	16	26	63	51	87	35	9	23

Figure S365. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S366. Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
8P LOSS MUTATED	48	45	58	39	13
8P LOSS WILD-TYPE	53	107	56	49	45

Figure S366. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S367. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
8P LOSS MUTATED	124	94	19	140	22
8P LOSS WILD-TYPE	136	318	74	125	27

Figure S367. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S368. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
8P LOSS MUTATED	58	54	80	15	49
8P LOSS WILD-TYPE	74	143	97	73	79

Figure S368. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S369. Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
8P LOSS MUTATED	11	50	40	50	15
8P LOSS WILD-TYPE	53	56	50	57	16

Figure S369. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S370. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
8P LOSS MUTATED	200	137	58
8P LOSS WILD-TYPE	343	161	174

Figure S370. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S371. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
8P LOSS MUTATED	92	85	92	18	74	34
8P LOSS WILD-TYPE	127	79	214	123	109	26

Figure S371. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S372. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
8P LOSS MUTATED	154	75	164
8P LOSS WILD-TYPE	177	178	312

Figure S372. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S373. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
8P LOSS MUTATED	98	80	88	38	30	59
8P LOSS WILD-TYPE	133	80	234	89	56	75

Figure S373. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S374. Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9P LOSS MUTATED	7	10	53	30	18	33	10	6
9P LOSS WILD-TYPE	14	26	66	66	91	39	10	34

Figure S374. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S375. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
9P LOSS MUTATED	43	31	59	25	9
9P LOSS WILD-TYPE	58	121	55	63	49

Figure S375. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S376. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
9P LOSS MUTATED	143	40	15	101	13
9P LOSS WILD-TYPE	117	372	78	164	36

Figure S376. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S377. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
9P LOSS MUTATED	49	41	76	13	24
9P LOSS WILD-TYPE	83	156	101	75	104

Figure S377. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S378. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
9P LOSS MUTATED	182	99	30
9P LOSS WILD-TYPE	361	199	202

Figure S378. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S379. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
9P LOSS MUTATED	94	77	53	13	50	24
9P LOSS WILD-TYPE	125	87	253	128	133	36

Figure S379. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S380. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
9P LOSS MUTATED	130	39	137
9P LOSS WILD-TYPE	201	214	339

Figure S380. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S381. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
9P LOSS MUTATED	98	70	46	35	21	36
9P LOSS WILD-TYPE	133	90	276	92	65	98

Figure S381. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.057

Table S382. Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
9P LOSS MUTATED	65	52	21	19	28
9P LOSS WILD-TYPE	115	87	78	92	105

Figure S382. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S383. Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
9P LOSS MUTATED	119	48	18
9P LOSS WILD-TYPE	186	199	92

Figure S383. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.048

Table S384. Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
9Q LOSS MUTATED	7	5	41	41	19	23	8	5
9Q LOSS WILD-TYPE	14	31	78	55	90	49	12	35

Figure S384. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S385. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
9Q LOSS MUTATED	36	23	47	35	8
9Q LOSS WILD-TYPE	65	129	67	53	50

Figure S385. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S386. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
9Q LOSS MUTATED	112	36	14	106	14
9Q LOSS WILD-TYPE	148	376	79	159	35

Figure S386. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S387. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
9Q LOSS MUTATED	59	40	57	10	22
9Q LOSS WILD-TYPE	73	157	120	78	106

Figure S387. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S388. Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
9Q LOSS MUTATED	66	28	23
9Q LOSS WILD-TYPE	83	104	94

Figure S388. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S389. Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
9Q LOSS MUTATED	11	21	40	33	12
9Q LOSS WILD-TYPE	53	85	50	74	19

Figure S389. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S390. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
9Q LOSS MUTATED	151	109	21
9Q LOSS WILD-TYPE	392	189	211

Figure S390. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S391. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
9Q LOSS MUTATED	77	61	43	13	68	19
9Q LOSS WILD-TYPE	142	103	263	128	115	41

Figure S391. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S392. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
9Q LOSS MUTATED	132	32	109
9Q LOSS WILD-TYPE	199	221	367

Figure S392. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S393. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
9Q LOSS MUTATED	78	64	31	28	19	53
9Q LOSS WILD-TYPE	153	96	291	99	67	81

Figure S393. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S394. Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
9Q LOSS MUTATED	51	57	19	15	24
9Q LOSS WILD-TYPE	129	82	80	96	109

Figure S394. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S395. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
9Q LOSS MUTATED	111	41	14
9Q LOSS WILD-TYPE	194	206	96

Figure S395. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S396. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
10P LOSS MUTATED	59	29	19	55	11
10P LOSS WILD-TYPE	201	383	74	210	38

Figure S396. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S397. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
10P LOSS MUTATED	35	31	35	12	8
10P LOSS WILD-TYPE	97	166	142	76	120

Figure S397. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S398. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
10P LOSS MUTATED	95	62	15
10P LOSS WILD-TYPE	448	236	217

Figure S398. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S399. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
10P LOSS MUTATED	45	41	29	14	32	11
10P LOSS WILD-TYPE	174	123	277	127	151	49

Figure S399. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S400. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
10Q LOSS MUTATED	70	33	19	92	15
10Q LOSS WILD-TYPE	190	379	74	173	34

Figure S400. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S401. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
10Q LOSS MUTATED	55	34	53	11	12
10Q LOSS WILD-TYPE	77	163	124	77	116

Figure S401. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S402. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
10Q LOSS MUTATED	114	96	18
10Q LOSS WILD-TYPE	429	202	214

Figure S402. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S403. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
10Q LOSS MUTATED	55	54	31	14	60	14
10Q LOSS WILD-TYPE	164	110	275	127	123	46

Figure S403. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.12

Table S404. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
10Q LOSS MUTATED	94	38	92
10Q LOSS WILD-TYPE	237	215	384

Figure S404. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S405. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
10Q LOSS MUTATED	60	53	38	18	13	42
10Q LOSS WILD-TYPE	171	107	284	109	73	92

Figure S405. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.048

Table S406. Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
10Q LOSS MUTATED	47	45	17	10	28
10Q LOSS WILD-TYPE	133	94	82	101	105

Figure S406. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S407. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
11P LOSS MUTATED	98	41	23	103	10
11P LOSS WILD-TYPE	162	371	70	162	39

Figure S407. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S408. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
11P LOSS MUTATED	47	35	64	13	20
11P LOSS WILD-TYPE	85	162	113	75	108

Figure S408. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S409. Gene #61: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
11P LOSS MUTATED	8	22	33	34	15
11P LOSS WILD-TYPE	56	84	57	73	16

Figure S409. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S410. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
11P LOSS MUTATED	149	99	27
11P LOSS WILD-TYPE	394	199	205

Figure S410. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S411. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
11P LOSS MUTATED	71	61	52	15	57	19
11P LOSS WILD-TYPE	148	103	254	126	126	41

Figure S411. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S412. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
11P LOSS MUTATED	113	46	108
11P LOSS WILD-TYPE	218	207	368

Figure S412. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S413. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
11P LOSS MUTATED	81	52	49	26	17	42
11P LOSS WILD-TYPE	150	108	273	101	69	92

Figure S413. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S414. Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
11Q LOSS MUTATED	5	16	65	26	25	27	6	15
11Q LOSS WILD-TYPE	16	20	54	70	84	45	14	25

Figure S414. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S415. Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
11Q LOSS MUTATED	58	49	41	24	13
11Q LOSS WILD-TYPE	43	103	73	64	45

Figure S415. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S416. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
11Q LOSS MUTATED	151	75	29	96	13
11Q LOSS WILD-TYPE	109	337	64	169	36

Figure S416. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S417. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
11Q LOSS MUTATED	44	67	83	21	27
11Q LOSS WILD-TYPE	88	130	94	67	101

Figure S417. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S418. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
11Q LOSS MUTATED	215	90	58
11Q LOSS WILD-TYPE	328	208	174

Figure S418. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S419. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
11Q LOSS MUTATED	113	64	94	22	53	17
11Q LOSS WILD-TYPE	106	100	212	119	130	43

Figure S419. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S420. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
12P LOSS MUTATED	36	31	11	71	2
12P LOSS WILD-TYPE	224	381	82	194	47

Figure S420. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S421. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
12P LOSS MUTATED	41	16	21	12	11
12P LOSS WILD-TYPE	91	181	156	76	117

Figure S421. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S422. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
12P LOSS MUTATED	51	79	20
12P LOSS WILD-TYPE	492	219	212

Figure S422. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S423. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
12P LOSS MUTATED	24	25	26	10	50	15
12P LOSS WILD-TYPE	195	139	280	131	133	45

Figure S423. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S424. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
12P LOSS MUTATED	77	24	48
12P LOSS WILD-TYPE	254	229	428

Figure S424. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S425. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
12P LOSS MUTATED	33	33	26	10	10	37
12P LOSS WILD-TYPE	198	127	296	117	76	97

Figure S425. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S426. Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
12P LOSS MUTATED	22	45	9	11	9
12P LOSS WILD-TYPE	158	94	90	100	124

Figure S426. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S427. Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
12P LOSS MUTATED	69	16	11
12P LOSS WILD-TYPE	236	231	99

Figure S427. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S428. Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
12Q LOSS MUTATED	2	3	7	33	5	5	2	3
12Q LOSS WILD-TYPE	19	33	112	63	104	67	18	37

Figure S428. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S429. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
12Q LOSS MUTATED	5	8	15	28	4
12Q LOSS WILD-TYPE	96	144	99	60	54

Figure S429. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S430. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
12Q LOSS MUTATED	19	20	9	80	3
12Q LOSS WILD-TYPE	241	392	84	185	46

Figure S430. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S431. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
12Q LOSS MUTATED	51	9	17	6	8
12Q LOSS WILD-TYPE	81	188	160	82	120

Figure S431. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S432. Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
12Q LOSS MUTATED	32	9	8
12Q LOSS WILD-TYPE	117	123	109

Figure S432. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S433. Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
12Q LOSS MUTATED	8	5	28	4	4
12Q LOSS WILD-TYPE	56	101	62	103	27

Figure S433. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S434. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
12Q LOSS MUTATED	33	84	13
12Q LOSS WILD-TYPE	510	214	219

Figure S434. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S435. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
12Q LOSS MUTATED	13	16	19	6	63	13
12Q LOSS WILD-TYPE	206	148	287	135	120	47

Figure S435. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S436. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
12Q LOSS MUTATED	80	18	30
12Q LOSS WILD-TYPE	251	235	446

Figure S436. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S437. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
12Q LOSS MUTATED	21	30	16	8	6	47
12Q LOSS WILD-TYPE	210	130	306	119	80	87

Figure S437. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S438. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
12Q LOSS MUTATED	15	53	6	10	11
12Q LOSS WILD-TYPE	165	86	93	101	122

Figure S438. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S439. Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
12Q LOSS MUTATED	72	16	7
12Q LOSS WILD-TYPE	233	231	103

Figure S439. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S440. Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
13Q LOSS MUTATED	7	14	62	51	30	38	9	8
13Q LOSS WILD-TYPE	14	22	57	45	79	34	11	32

Figure S440. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S441. Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
13Q LOSS MUTATED	58	40	62	47	12
13Q LOSS WILD-TYPE	43	112	52	41	46

Figure S441. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S442. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
13Q LOSS MUTATED	141	80	47	137	27
13Q LOSS WILD-TYPE	119	332	46	128	22

Figure S442. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S443. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
13Q LOSS MUTATED	76	70	87	18	39
13Q LOSS WILD-TYPE	56	127	90	70	89

Figure S443. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S444. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
13Q LOSS MUTATED	219	155	57
13Q LOSS WILD-TYPE	324	143	175

Figure S444. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S445. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
13Q LOSS MUTATED	99	84	97	30	98	23
13Q LOSS WILD-TYPE	120	80	209	111	85	37

Figure S445. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S446. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
13Q LOSS MUTATED	169	73	183
13Q LOSS WILD-TYPE	162	180	293

Figure S446. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S447. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
13Q LOSS MUTATED	112	71	96	42	32	72
13Q LOSS WILD-TYPE	119	89	226	85	54	62

Figure S447. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S448. Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
13Q LOSS MUTATED	78	74	29	24	44
13Q LOSS WILD-TYPE	102	65	70	87	89

Figure S448. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.17

Table S449. Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
13Q LOSS MUTATED	139	78	32
13Q LOSS WILD-TYPE	166	169	78

Figure S449. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S450. Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
14Q LOSS MUTATED	3	1	30	50	7	14	9	5
14Q LOSS WILD-TYPE	18	35	89	46	102	58	11	35

Figure S450. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S451. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
14Q LOSS MUTATED	24	17	29	47	2
14Q LOSS WILD-TYPE	77	135	85	41	56

Figure S451. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S452. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
14Q LOSS MUTATED	63	34	19	139	11
14Q LOSS WILD-TYPE	197	378	74	126	38

Figure S452. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S453. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
14Q LOSS MUTATED	78	24	40	11	28
14Q LOSS WILD-TYPE	54	173	137	77	100

Figure S453. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S454. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
14Q LOSS MUTATED	54	16	25
14Q LOSS WILD-TYPE	95	116	92

Figure S454. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S455. Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
14Q LOSS MUTATED	4	20	44	22	5
14Q LOSS WILD-TYPE	60	86	46	85	26

Figure S455. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S456. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
14Q LOSS MUTATED	99	143	23
14Q LOSS WILD-TYPE	444	155	209

Figure S456. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S457. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
14Q LOSS MUTATED	39	55	38	12	109	12
14Q LOSS WILD-TYPE	180	109	268	129	74	48

Figure S457. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S458. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
14Q LOSS MUTATED	147	39	73
14Q LOSS WILD-TYPE	184	214	403

Figure S458. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S459. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
14Q LOSS MUTATED	54	56	38	16	9	86
14Q LOSS WILD-TYPE	177	104	284	111	77	48

Figure S459. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S460. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
14Q LOSS MUTATED	35	78	19	17	24
14Q LOSS WILD-TYPE	145	61	80	94	109

Figure S460. Get High-res Image Gene #66: '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 = 0.0096

Table S461. Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
14Q LOSS MUTATED	113	44	16
14Q LOSS WILD-TYPE	192	203	94

Figure S461. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S462. Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
15Q LOSS MUTATED	4	9	32	45	22	33	8	6
15Q LOSS WILD-TYPE	17	27	87	51	87	39	12	34

Figure S462. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S463. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
15Q LOSS MUTATED	27	29	48	43	12
15Q LOSS WILD-TYPE	74	123	66	45	46

Figure S463. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S464. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
15Q LOSS MUTATED	85	40	43	136	15
15Q LOSS WILD-TYPE	175	372	50	129	34

Figure S464. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S465. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
15Q LOSS MUTATED	74	39	59	15	28
15Q LOSS WILD-TYPE	58	158	118	73	100

Figure S465. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S466. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
15Q LOSS MUTATED	157	135	25
15Q LOSS WILD-TYPE	386	163	207

Figure S466. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S467. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
15Q LOSS MUTATED	64	67	52	24	94	16
15Q LOSS WILD-TYPE	155	97	254	117	89	44

Figure S467. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S468. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
15Q LOSS MUTATED	149	40	121
15Q LOSS WILD-TYPE	182	213	355

Figure S468. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S469. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
15Q LOSS MUTATED	72	65	44	42	16	71
15Q LOSS WILD-TYPE	159	95	278	85	70	63

Figure S469. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S470. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
15Q LOSS MUTATED	55	71	23	21	21
15Q LOSS WILD-TYPE	125	68	76	90	112

Figure S470. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S471. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
15Q LOSS MUTATED	114	47	30
15Q LOSS WILD-TYPE	191	200	80

Figure S471. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S472. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
16P LOSS MUTATED	37	49	11	66	10
16P LOSS WILD-TYPE	223	363	82	199	39

Figure S472. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S473. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
16P LOSS MUTATED	35	23	45	12	50	7
16P LOSS WILD-TYPE	184	141	261	129	133	53

Figure S473. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S474. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
16P LOSS MUTATED	78	34	59
16P LOSS WILD-TYPE	253	219	417

Figure S474. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.097

Table S475. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
16P LOSS MUTATED	22	42	12	13	21
16P LOSS WILD-TYPE	158	97	87	98	112

Figure S475. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S476. Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16Q LOSS MUTATED	12	21	63	28	81	38	11	30
16Q LOSS WILD-TYPE	9	15	56	68	28	34	9	10

Figure S476. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S477. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
16Q LOSS MUTATED	58	102	58	24	42
16Q LOSS WILD-TYPE	43	50	56	64	16

Figure S477. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S478. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
16Q LOSS MUTATED	135	245	70	112	31
16Q LOSS WILD-TYPE	125	167	23	153	18

Figure S478. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S479. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
16Q LOSS MUTATED	52	131	103	57	57
16Q LOSS WILD-TYPE	80	66	74	31	71

Figure S479. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S480. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
16Q LOSS MUTATED	60	84	66
16Q LOSS WILD-TYPE	89	48	51

Figure S480. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S481. Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
16Q LOSS MUTATED	47	60	28	64	11
16Q LOSS WILD-TYPE	17	46	62	43	20

Figure S481. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S482. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
16Q LOSS MUTATED	330	108	151
16Q LOSS WILD-TYPE	213	190	81

Figure S482. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S483. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
16Q LOSS MUTATED	124	86	205	93	64	17
16Q LOSS WILD-TYPE	95	78	101	48	119	43

Figure S483. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S484. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
16Q LOSS MUTATED	130	152	301
16Q LOSS WILD-TYPE	201	101	175

Figure S484. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S485. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
16Q LOSS MUTATED	116	56	206	100	50	55
16Q LOSS WILD-TYPE	115	104	116	27	36	79

Figure S485. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.034

Table S486. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
16Q LOSS MUTATED	139	153	70
16Q LOSS WILD-TYPE	166	94	40

Figure S486. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S487. Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17P LOSS MUTATED	13	23	66	61	30	57	12	21
17P LOSS WILD-TYPE	8	13	53	35	79	15	8	19

Figure S487. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S488. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
17P LOSS MUTATED	57	76	85	54	11
17P LOSS WILD-TYPE	44	76	29	34	47

Figure S488. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S489. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
17P LOSS MUTATED	172	142	41	198	26
17P LOSS WILD-TYPE	88	270	52	67	23

Figure S489. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S490. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
17P LOSS MUTATED	82	90	112	37	52
17P LOSS WILD-TYPE	50	107	65	51	76

Figure S490. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S491. Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
17P LOSS MUTATED	109	55	56
17P LOSS WILD-TYPE	40	77	61

Figure S491. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S492. Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
17P LOSS MUTATED	21	47	61	68	23
17P LOSS WILD-TYPE	43	59	29	39	8

Figure S492. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S493. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
17P LOSS MUTATED	279	198	99
17P LOSS WILD-TYPE	264	100	133

Figure S493. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S494. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
17P LOSS MUTATED	119	123	156	26	109	43
17P LOSS WILD-TYPE	100	41	150	115	74	17

Figure S494. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S495. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
17P LOSS MUTATED	219	110	240
17P LOSS WILD-TYPE	112	143	236

Figure S495. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S496. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
17P LOSS MUTATED	139	95	149	67	29	90
17P LOSS WILD-TYPE	92	65	173	60	57	44

Figure S496. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S497. Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q LOSS MUTATED	4	4	23	50	12	35	4	12
17Q LOSS WILD-TYPE	17	32	96	46	97	37	16	28

Figure S497. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S498. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
17Q LOSS MUTATED	21	26	48	44	5
17Q LOSS WILD-TYPE	80	126	66	44	53

Figure S498. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S499. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
17Q LOSS MUTATED	57	55	24	132	7
17Q LOSS WILD-TYPE	203	357	69	133	42

Figure S499. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S500. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
17Q LOSS MUTATED	64	26	32	11	30
17Q LOSS WILD-TYPE	68	171	145	77	98

Figure S500. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S501. Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
17Q LOSS MUTATED	72	16	30
17Q LOSS WILD-TYPE	77	116	87

Figure S501. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S502. Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
17Q LOSS MUTATED	8	23	50	22	15
17Q LOSS WILD-TYPE	56	83	40	85	16

Figure S502. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S503. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
17Q LOSS MUTATED	101	136	36
17Q LOSS WILD-TYPE	442	162	196

Figure S503. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S504. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
17Q LOSS MUTATED	33	59	61	5	83	32
17Q LOSS WILD-TYPE	186	105	245	136	100	28

Figure S504. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S505. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
17Q LOSS MUTATED	135	47	88
17Q LOSS WILD-TYPE	196	206	388

Figure S505. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S506. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
17Q LOSS MUTATED	62	61	47	27	5	68
17Q LOSS WILD-TYPE	169	99	275	100	81	66

Figure S506. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S507. Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
17Q LOSS MUTATED	37	58	16	23	32
17Q LOSS WILD-TYPE	143	81	83	88	101

Figure S507. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.12

Table S508. Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18P LOSS MUTATED	6	11	35	27	19	38	9	13
18P LOSS WILD-TYPE	15	25	84	69	90	34	11	27

Figure S508. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.17

Table S509. Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18P LOSS MUTATED	28	39	55	24	12
18P LOSS WILD-TYPE	73	113	59	64	46

Figure S509. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S510. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
18P LOSS MUTATED	108	66	34	100	12
18P LOSS WILD-TYPE	152	346	59	165	37

Figure S510. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S511. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18P LOSS MUTATED	36	39	88	16	31
18P LOSS WILD-TYPE	96	158	89	72	97

Figure S511. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.16

Table S512. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
18P LOSS MUTATED	164	107	47
18P LOSS WILD-TYPE	379	191	185

Figure S512. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S513. Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
18P LOSS MUTATED	59	88	79	19	50	23
18P LOSS WILD-TYPE	160	76	227	122	133	37

Figure S513. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S514. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
18P LOSS MUTATED	99	57	76	33	18	34
18P LOSS WILD-TYPE	132	103	246	94	68	100

Figure S514. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.11

Table S515. Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18Q LOSS MUTATED	5	11	34	26	19	38	7	9
18Q LOSS WILD-TYPE	16	25	85	70	90	34	13	31

Figure S515. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S516. Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18Q LOSS MUTATED	27	34	53	24	11
18Q LOSS WILD-TYPE	74	118	61	64	47

Figure S516. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S517. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
18Q LOSS MUTATED	106	65	35	104	11
18Q LOSS WILD-TYPE	154	347	58	161	38

Figure S517. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S518. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18Q LOSS MUTATED	45	42	86	15	28
18Q LOSS WILD-TYPE	87	155	91	73	100

Figure S518. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S519. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
18Q LOSS MUTATED	164	110	44
18Q LOSS WILD-TYPE	379	188	188

Figure S519. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S520. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
18Q LOSS MUTATED	51	89	78	19	56	25
18Q LOSS WILD-TYPE	168	75	228	122	127	35

Figure S520. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S521. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
18Q LOSS MUTATED	90	67	73	31	16	39
18Q LOSS WILD-TYPE	141	93	249	96	70	95

Figure S521. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S522. Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19P LOSS MUTATED	2	6	30	20	8	25	1	2
19P LOSS WILD-TYPE	19	30	89	76	101	47	19	38

Figure S522. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S523. Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
19P LOSS MUTATED	29	13	32	18	2
19P LOSS WILD-TYPE	72	139	82	70	56

Figure S523. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S524. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
19P LOSS MUTATED	89	19	9	68	8
19P LOSS WILD-TYPE	171	393	84	197	41

Figure S524. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S525. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
19P LOSS MUTATED	36	21	47	5	15
19P LOSS WILD-TYPE	96	176	130	83	113

Figure S525. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S526. Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
19P LOSS MUTATED	3	13	21	27	11
19P LOSS WILD-TYPE	61	93	69	80	20

Figure S526. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S527. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
19P LOSS MUTATED	105	75	12
19P LOSS WILD-TYPE	438	223	220

Figure S527. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S528. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
19P LOSS MUTATED	50	57	23	8	44	10
19P LOSS WILD-TYPE	169	107	283	133	139	50

Figure S528. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S529. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
19P LOSS MUTATED	97	19	72
19P LOSS WILD-TYPE	234	234	404

Figure S529. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S530. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
19P LOSS MUTATED	59	40	19	19	18	33
19P LOSS WILD-TYPE	172	120	303	108	68	101

Figure S530. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S531. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
19P LOSS MUTATED	37	41	13	6	20
19P LOSS WILD-TYPE	143	98	86	105	113

Figure S531. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S532. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
19P LOSS MUTATED	77	34	6
19P LOSS WILD-TYPE	228	213	104

Figure S532. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S533. Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
19Q LOSS MUTATED	23	10	29	11	2
19Q LOSS WILD-TYPE	78	142	85	77	56

Figure S533. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S534. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
19Q LOSS MUTATED	80	16	6	51	8
19Q LOSS WILD-TYPE	180	396	87	214	41

Figure S534. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S535. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
19Q LOSS MUTATED	27	17	43	2	15
19Q LOSS WILD-TYPE	105	180	134	86	113

Figure S535. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S536. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
19Q LOSS MUTATED	90	61	9
19Q LOSS WILD-TYPE	453	237	223

Figure S536. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S537. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
19Q LOSS MUTATED	46	43	19	8	34	10
19Q LOSS WILD-TYPE	173	121	287	133	149	50

Figure S537. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S538. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
19Q LOSS MUTATED	76	19	62
19Q LOSS WILD-TYPE	255	234	414

Figure S538. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S539. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
19Q LOSS MUTATED	49	26	16	17	20	29
19Q LOSS WILD-TYPE	182	134	306	110	66	105

Figure S539. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S540. Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
19Q LOSS MUTATED	30	34	10	6	16
19Q LOSS WILD-TYPE	150	105	89	105	117

Figure S540. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S541. Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
19Q LOSS MUTATED	65	27	4
19Q LOSS WILD-TYPE	240	220	106

Figure S541. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.043

Table S542. Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
20P LOSS MUTATED	9	4	12	14	0
20P LOSS WILD-TYPE	92	148	102	74	58

Figure S542. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S543. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
20P LOSS MUTATED	25	10	5	49	4
20P LOSS WILD-TYPE	235	402	88	216	45

Figure S543. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S544. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
20P LOSS MUTATED	33	6	17	5	4
20P LOSS WILD-TYPE	99	191	160	83	124

Figure S544. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S545. Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
20P LOSS MUTATED	37	53	3
20P LOSS WILD-TYPE	506	245	229

Figure S545. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S546. Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
20P LOSS MUTATED	17	22	6	3	41	4
20P LOSS WILD-TYPE	202	142	300	138	142	56

Figure S546. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S547. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
20P LOSS MUTATED	51	13	23
20P LOSS WILD-TYPE	280	240	453

Figure S547. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S548. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
20P LOSS MUTATED	22	11	10	6	6	32
20P LOSS WILD-TYPE	209	149	312	121	80	102

Figure S548. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S549. Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
20P LOSS MUTATED	8	28	6	4	5
20P LOSS WILD-TYPE	172	111	93	107	128

Figure S549. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.038

Table S550. Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
20P LOSS MUTATED	37	13	1
20P LOSS WILD-TYPE	268	234	109

Figure S550. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S551. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
20Q LOSS MUTATED	10	5	5	32	3
20Q LOSS WILD-TYPE	250	407	88	233	46

Figure S551. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S552. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
20Q LOSS MUTATED	24	5	4	3	2
20Q LOSS WILD-TYPE	108	192	173	85	126

Figure S552. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S553. Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
20Q LOSS MUTATED	16	36	3
20Q LOSS WILD-TYPE	527	262	229

Figure S553. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S554. Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
20Q LOSS MUTATED	8	9	4	1	31	2
20Q LOSS WILD-TYPE	211	155	302	140	152	58

Figure S554. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S555. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
20Q LOSS MUTATED	32	11	9
20Q LOSS WILD-TYPE	299	242	467

Figure S555. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S556. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
20Q LOSS MUTATED	7	9	8	3	2	23
20Q LOSS WILD-TYPE	224	151	314	124	84	111

Figure S556. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S557. Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
20Q LOSS MUTATED	2	22	2	2	3
20Q LOSS WILD-TYPE	178	117	97	109	130

Figure S557. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S558. Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
20Q LOSS MUTATED	25	6	0
20Q LOSS WILD-TYPE	280	241	110

Figure S558. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S559. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
21Q LOSS MUTATED	74	24	17	55	10
21Q LOSS WILD-TYPE	186	388	76	210	39

Figure S559. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S560. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
22Q LOSS MUTATED	148	134	59	117	24
22Q LOSS WILD-TYPE	112	278	34	148	25

Figure S560. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.034

Table S561. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
22Q LOSS MUTATED	279	109	91
22Q LOSS WILD-TYPE	264	189	141

Figure S561. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S562. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
22Q LOSS MUTATED	119	92	131	52	70	15
22Q LOSS WILD-TYPE	100	72	175	89	113	45

Figure S562. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S563. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
XQ LOSS MUTATED	67	28	14	70	6
XQ LOSS WILD-TYPE	193	384	79	195	43

Figure S563. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S564. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
XQ LOSS MUTATED	31	29	45	6	9
XQ LOSS WILD-TYPE	101	168	132	82	119

Figure S564. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S565. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
XQ LOSS MUTATED	101	63	20
XQ LOSS WILD-TYPE	442	235	212

Figure S565. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S566. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
XQ LOSS MUTATED	49	42	33	15	39	6
XQ LOSS WILD-TYPE	170	122	273	126	144	54

Figure S566. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.15

Table S567. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
XQ LOSS MUTATED	76	27	79
XQ LOSS WILD-TYPE	255	226	397

Figure S567. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 1079
Number of significantly arm-level cnvs = 80
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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