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

Glioma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C15Q4V32

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 1090 patients, 496 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 496 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	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
7p gain	595 (55%)	495	3e-05 (0.000166)	1e-05 (6.15e-05)	0.00071 (0.00264)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00284 (0.00907)	1e-05 (6.15e-05)	0.00023 (0.000971)	1e-05 (6.15e-05)
7q gain	631 (58%)	459	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00221 (0.00722)	0.00011 (0.000515)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00842 (0.0232)	1e-05 (6.15e-05)	0.00093 (0.00338)	1e-05 (6.15e-05)
20q gain	263 (24%)	827	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00296 (0.00937)	2e-05 (0.000114)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0253 (0.0581)	1e-05 (6.15e-05)	0.00016 (0.000709)	1e-05 (6.15e-05)
10p loss	563 (52%)	527	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0128 (0.0329)	0.00011 (0.000515)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	4e-05 (0.00021)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)
10q loss	591 (54%)	499	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00304 (0.00959)	0.00016 (0.000709)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	3e-05 (0.000166)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)
19q gain	222 (20%)	868	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.162 (0.256)	0.00974 (0.0261)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00113 (0.00396)	1e-05 (6.15e-05)	2e-05 (0.000114)	1e-05 (6.15e-05)
20p gain	266 (24%)	824	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00448 (0.0133)	2e-05 (0.000114)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.117 (0.197)	1e-05 (6.15e-05)	0.00262 (0.00851)	1e-05 (6.15e-05)
4q loss	151 (14%)	939	0.00026 (0.00109)	0.00018 (0.000791)	0.0307 (0.0669)	0.1 (0.173)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00931 (0.0252)	7e-05 (0.000353)	0.00014 (0.000638)	0.00389 (0.0117)	1e-05 (6.15e-05)	4e-05 (0.00021)
19p gain	323 (30%)	767	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0844 (0.15)	0.00036 (0.00146)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00135 (0.00461)	0.0313 (0.0679)	0.282 (0.393)	0.00783 (0.0217)
11p loss	163 (15%)	927	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.792 (0.845)	0.014 (0.0354)	0.00112 (0.00394)	1e-05 (6.15e-05)	0.00034 (0.00139)	1e-05 (6.15e-05)	2e-05 (0.000114)	5e-05 (0.000258)	0.349 (0.465)	0.0172 (0.0424)
14q loss	225 (21%)	865	2e-05 (0.000114)	0.0001 (0.000475)	0.51 (0.62)	0.539 (0.641)	1e-05 (6.15e-05)	0.00011 (0.000515)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00319 (0.00993)	0.00184 (0.00606)	0.00857 (0.0235)	0.00074 (0.00274)
19q loss	244 (22%)	846	0.00665 (0.0187)	0.0114 (0.0299)	0.526 (0.632)	0.181 (0.279)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)
4p loss	127 (12%)	963	0.0453 (0.0918)	0.00163 (0.00547)	0.0637 (0.118)	0.176 (0.274)	0.0159 (0.0396)	1e-05 (6.15e-05)	0.0716 (0.13)	0.0018 (0.00594)	5e-05 (0.000258)	0.00022 (0.000937)	4e-05 (0.00021)	1e-05 (6.15e-05)
11q loss	113 (10%)	977	2e-05 (0.000114)	0.00019 (0.000824)	0.915 (0.941)	0.0768 (0.137)	1e-05 (6.15e-05)	5e-05 (0.000258)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0256 (0.0586)	0.00019 (0.000824)	0.332 (0.446)	0.001 (0.00357)
1p gain	95 (9%)	995	0.604 (0.7)	0.128 (0.21)	0.485 (0.598)	0.248 (0.355)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00576 (0.0165)	1e-05 (6.15e-05)	0.0126 (0.0325)	0.00019 (0.000824)
8q gain	118 (11%)	972	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0395 (0.0821)	0.453 (0.571)	0.0192 (0.0464)	1e-05 (6.15e-05)	0.117 (0.197)	0.00095 (0.00342)	0.159 (0.251)	0.0975 (0.169)	0.0344 (0.0734)	0.0109 (0.0287)
18q gain	75 (7%)	1015	1e-05 (6.15e-05)	0.00034 (0.00139)	0.121 (0.202)	0.389 (0.508)	0.00016 (0.000709)	0.0009 (0.00329)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.356 (0.473)	0.00897 (0.0244)	0.283 (0.393)	0.00112 (0.00394)
21q gain	88 (8%)	1002	0.00134 (0.00459)	0.00734 (0.0205)	0.0111 (0.0293)	0.00365 (0.0111)	3e-05 (0.000166)	0.0207 (0.0491)	0.00021 (0.000898)	1e-05 (6.15e-05)	0.622 (0.715)	0.099 (0.171)	0.725 (0.795)	0.0806 (0.143)
1p loss	199 (18%)	891	0.635 (0.727)	0.829 (0.875)	0.94 (0.96)	0.196 (0.297)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)
17p loss	77 (7%)	1013	0.0239 (0.0558)	0.0267 (0.0604)	0.664 (0.75)	0.485 (0.598)	1e-05 (6.15e-05)	0.00056 (0.00214)	1e-05 (6.15e-05)	2e-05 (0.000114)	0.159 (0.251)	0.00666 (0.0187)	0.712 (0.786)	0.0119 (0.0309)
3p gain	67 (6%)	1023	0.00017 (0.00075)	0.0126 (0.0325)	0.667 (0.75)	0.0295 (0.0658)	1e-05 (6.15e-05)	0.027 (0.0608)	0.00034 (0.00139)	0.00016 (0.000709)	0.0703 (0.128)	0.451 (0.57)	0.785 (0.841)	0.379 (0.495)
5p gain	60 (6%)	1030	0.114 (0.193)	0.158 (0.251)	0.176 (0.274)	0.347 (0.462)	1e-05 (6.15e-05)	0.00531 (0.0156)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0242 (0.0563)	0.0259 (0.0591)	0.143 (0.23)	0.0159 (0.0396)
5q gain	50 (5%)	1040	0.141 (0.229)	0.232 (0.339)	0.117 (0.197)	0.0538 (0.105)	1e-05 (6.15e-05)	0.00065 (0.00244)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.073 (0.132)	0.00586 (0.0168)	0.0453 (0.0918)	0.00501 (0.0147)
9p gain	64 (6%)	1026	0.00363 (0.0111)	0.0307 (0.0669)	0.705 (0.781)	0.434 (0.551)	1e-05 (6.15e-05)	0.018 (0.0439)	0.00048 (0.00187)	0.00044 (0.00174)	0.68 (0.76)	0.0269 (0.0607)	1 (1.00)	0.236 (0.343)
10p gain	70 (6%)	1020	0.001 (0.00357)	8e-05 (0.000392)	0.115 (0.195)	0.0593 (0.112)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0537 (0.105)	0.294 (0.404)	0.478 (0.593)	0.00469 (0.0139)
12q gain	66 (6%)	1024	0.522 (0.629)	0.955 (0.974)	0.535 (0.638)	0.0101 (0.0269)	8e-05 (0.000392)	0.04 (0.083)	0.00115 (0.004)	0.00127 (0.00438)	0.0192 (0.0464)	0.00385 (0.0116)	0.0552 (0.107)	0.0734 (0.132)
17q gain	86 (8%)	1004	0.00114 (0.00398)	0.0469 (0.0941)	0.126 (0.209)	0.0316 (0.0683)	9e-05 (0.000432)	0.292 (0.403)	0.00178 (0.0059)	0.0281 (0.0629)	0.0265 (0.0602)	0.474 (0.589)	0.129 (0.212)	0.191 (0.291)
18p gain	78 (7%)	1012	1e-05 (6.15e-05)	0.00047 (0.00184)	0.157 (0.25)	0.364 (0.48)	0.00224 (0.0073)	0.0164 (0.0408)	3e-05 (0.000166)	0.00041 (0.00163)	0.758 (0.821)	0.0773 (0.138)	0.747 (0.814)	0.0357 (0.0753)
5q loss	78 (7%)	1012	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00055 (0.00211)	0.148 (0.238)	0.00077 (0.00284)	0.0003 (0.00124)	0.066 (0.121)	0.00575 (0.0165)	0.00036 (0.00146)	0.301 (0.411)	0.809 (0.859)	0.881 (0.916)
6q loss	189 (17%)	901	0.938 (0.959)	0.642 (0.732)	0.564 (0.663)	0.842 (0.883)	1e-05 (6.15e-05)	9e-05 (0.000432)	5e-05 (0.000258)	1e-05 (6.15e-05)	0.00061 (0.00231)	0.168 (0.263)	0.0181 (0.0441)	9e-05 (0.000432)
8p loss	74 (7%)	1016	0.546 (0.647)	0.443 (0.561)	0.182 (0.28)	0.778 (0.836)	7e-05 (0.000353)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.0356 (0.0753)	0.00095 (0.00342)	0.762 (0.824)	0.0004 (0.0016)
8q loss	52 (5%)	1038	0.737 (0.805)	0.209 (0.313)	0.0369 (0.0773)	0.747 (0.814)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	2e-05 (0.000114)	1e-05 (6.15e-05)	0.0539 (0.105)	0.00052 (0.00201)	0.372 (0.487)	0.00012 (0.000554)
13q loss	298 (27%)	792	3e-05 (0.000166)	0.00175 (0.00582)	0.752 (0.817)	0.589 (0.686)	8e-05 (0.000392)	0.0171 (0.0421)	0.00046 (0.0018)	0.00041 (0.00163)	0.0617 (0.115)	0.00929 (0.0252)	0.225 (0.329)	0.26 (0.369)
17q loss	51 (5%)	1039	0.0048 (0.0141)	0.0614 (0.115)	0.249 (0.357)	0.0423 (0.0869)	0.0002 (0.000859)	0.00287 (0.00914)	0.00139 (0.00473)	0.00049 (0.0019)	0.162 (0.256)	0.265 (0.375)	1 (1.00)	0.0228 (0.0534)
22q loss	240 (22%)	850	0.624 (0.716)	0.584 (0.683)	0.158 (0.251)	0.83 (0.875)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.455 (0.573)	0.00027 (0.00113)	0.0118 (0.0306)	8e-05 (0.000392)
xp loss	213 (20%)	877	0.00624 (0.0177)	0.00795 (0.022)	0.0298 (0.066)	0.101 (0.174)	0.217 (0.321)	0.0715 (0.13)	0.00935 (0.0252)	0.0134 (0.0343)	0.0378 (0.0792)	0.243 (0.352)	0.0383 (0.08)	0.113 (0.192)
1q gain	112 (10%)	978	0.0764 (0.137)	0.0888 (0.157)	0.131 (0.214)	0.625 (0.716)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.12 (0.201)	0.0305 (0.0669)	0.0303 (0.0669)	0.0579 (0.11)
2q gain	48 (4%)	1042	0.664 (0.75)	0.909 (0.938)	0.0493 (0.0979)	0.204 (0.306)	0.00376 (0.0114)	0.057 (0.109)	0.00392 (0.0118)	0.00066 (0.00247)	0.513 (0.621)	0.0175 (0.0428)	0.683 (0.761)	0.0461 (0.0927)
3q gain	71 (7%)	1019	0.00023 (0.000971)	0.0345 (0.0736)	0.923 (0.946)	0.0658 (0.121)	1e-05 (6.15e-05)	0.00064 (0.00241)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.341 (0.457)	0.136 (0.221)	0.329 (0.443)	0.149 (0.24)
9q gain	96 (9%)	994	0.0493 (0.0979)	0.0501 (0.0991)	0.525 (0.632)	0.129 (0.212)	4e-05 (0.00021)	0.0141 (0.0354)	0.00014 (0.000638)	0.00308 (0.00968)	0.294 (0.404)	0.0105 (0.0279)	0.606 (0.7)	0.121 (0.201)
11q gain	74 (7%)	1016	0.123 (0.204)	0.0651 (0.12)	0.456 (0.573)	0.244 (0.353)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	4e-05 (0.00021)	1e-05 (6.15e-05)	0.62 (0.714)	0.0384 (0.0801)	0.754 (0.818)	0.0315 (0.0683)
5p loss	79 (7%)	1011	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.00071 (0.00264)	0.0737 (0.133)	0.00038 (0.00153)	7e-05 (0.000353)	0.151 (0.242)	0.0439 (0.0894)	0.188 (0.287)	0.457 (0.573)	0.739 (0.806)	0.502 (0.613)
6p loss	116 (11%)	974	0.575 (0.673)	0.42 (0.541)	0.778 (0.836)	0.648 (0.735)	1e-05 (6.15e-05)	0.00012 (0.000554)	1e-05 (6.15e-05)	1e-05 (6.15e-05)	0.541 (0.642)	0.233 (0.339)	0.00337 (0.0105)	0.00126 (0.00437)
9p loss	319 (29%)	771	0.00347 (0.0107)	0.112 (0.191)	0.528 (0.634)	0.393 (0.511)	4e-05 (0.00021)	1e-05 (6.15e-05)	0.00658 (0.0186)	0.0108 (0.0285)	0.891 (0.925)	0.22 (0.324)	0.281 (0.393)	0.0344 (0.0734)
15q loss	156 (14%)	934	6e-05 (0.000307)	1e-05 (6.15e-05)	0.00394 (0.0118)	0.00352 (0.0109)	0.045 (0.0915)	0.00146 (0.00494)	0.0501 (0.0991)	0.512 (0.621)	0.166 (0.26)	0.486 (0.598)	0.0521 (0.103)	0.0636 (0.118)
16q loss	105 (10%)	985	0.0596 (0.112)	0.426 (0.546)	0.465 (0.58)	0.897 (0.928)	1e-05 (6.15e-05)	2e-05 (0.000114)	2e-05 (0.000114)	2e-05 (0.000114)	0.667 (0.75)	0.00366 (0.0111)	0.293 (0.403)	0.00867 (0.0237)
xq loss	174 (16%)	916	0.0171 (0.0421)	0.0252 (0.0581)	0.119 (0.2)	0.122 (0.203)	0.625 (0.716)	0.00271 (0.00877)	0.00103 (0.00365)	0.142 (0.23)	9e-05 (0.000432)	0.352 (0.468)	0.108 (0.183)	0.0296 (0.0658)
2p gain	51 (5%)	1039	0.468 (0.582)	0.733 (0.803)	0.25 (0.357)	0.225 (0.329)	0.001 (0.00357)	0.25 (0.357)	0.00313 (0.00978)	0.00214 (0.00702)	0.601 (0.698)	0.0203 (0.0483)	0.892 (0.925)	0.0416 (0.0858)
11p gain	50 (5%)	1040	0.904 (0.933)	0.882 (0.916)	0.645 (0.733)	0.945 (0.965)	0.0136 (0.0345)	0.0001 (0.000475)	0.0971 (0.169)	0.0117 (0.0305)	0.0931 (0.163)	0.0117 (0.0305)	0.247 (0.355)	0.00356 (0.0109)
12p gain	94 (9%)	996	0.672 (0.753)	0.792 (0.845)	0.644 (0.732)	0.168 (0.263)	0.089 (0.157)	0.00274 (0.00884)	0.00448 (0.0133)	0.02 (0.0481)	0.0319 (0.0687)	0.00784 (0.0217)	0.0893 (0.158)	0.509 (0.619)
17p gain	72 (7%)	1018	0.00015 (0.00068)	0.0105 (0.0279)	0.0596 (0.112)	0.0203 (0.0483)	0.0017 (0.00567)	0.463 (0.578)	0.0403 (0.0834)	0.294 (0.404)	0.0928 (0.163)	0.717 (0.789)	0.427 (0.546)	0.452 (0.571)
22q gain	55 (5%)	1035	1e-05 (6.15e-05)	0.00656 (0.0185)	0.311 (0.423)	0.315 (0.427)	0.686 (0.763)	1e-05 (6.15e-05)	0.4 (0.519)	0.0136 (0.0345)	0.119 (0.199)	0.526 (0.632)	0.0423 (0.0869)	0.222 (0.327)
xq gain	59 (5%)	1031	0.429 (0.547)	0.966 (0.983)	0.921 (0.945)	0.515 (0.622)	0.00311 (0.00975)	1e-05 (6.15e-05)	0.0433 (0.0883)	0.00061 (0.00231)	0.0607 (0.114)	0.462 (0.578)	0.841 (0.883)	0.0218 (0.0515)
3p loss	71 (7%)	1019	0.839 (0.883)	0.916 (0.942)	0.795 (0.846)	0.17 (0.265)	0.82 (0.869)	0.248 (0.355)	0.0264 (0.0599)	0.0432 (0.0883)	0.00092 (0.00335)	0.00046 (0.0018)	0.198 (0.3)	0.00283 (0.00907)
9q loss	143 (13%)	947	0.167 (0.262)	0.0321 (0.0689)	0.13 (0.213)	0.187 (0.286)	0.025 (0.0579)	0.191 (0.291)	0.00551 (0.016)	0.025 (0.0579)	0.423 (0.543)	0.676 (0.757)	0.514 (0.621)	0.0206 (0.049)
4p gain	47 (4%)	1043	0.366 (0.481)	0.752 (0.817)	0.592 (0.689)	0.487 (0.598)	0.0582 (0.11)	0.0428 (0.0878)	0.00281 (0.00904)	0.00029 (0.00121)	0.253 (0.36)	0.0458 (0.0923)	0.308 (0.42)	0.282 (0.393)
4q gain	40 (4%)	1050	0.585 (0.684)	0.318 (0.43)	0.531 (0.635)	0.542 (0.643)	0.0291 (0.065)	0.00594 (0.0169)	1e-05 (6.15e-05)	4e-05 (0.00021)	0.219 (0.323)	0.0553 (0.107)	0.232 (0.338)	0.0668 (0.122)
6p gain	35 (3%)	1055	0.0153 (0.0383)	0.0984 (0.171)	0.895 (0.927)	0.282 (0.393)	0.0688 (0.126)	0.0223 (0.0523)	0.142 (0.229)	0.28 (0.393)	0.0113 (0.0296)	0.0232 (0.0542)	0.342 (0.457)	0.287 (0.397)
6q gain	28 (3%)	1062	0.00168 (0.00562)	0.0366 (0.077)	0.785 (0.841)	0.104 (0.178)	0.0301 (0.0665)	0.126 (0.208)	0.367 (0.481)	0.301 (0.412)	0.00609 (0.0173)	0.151 (0.242)	1 (1.00)	0.871 (0.909)
8p gain	101 (9%)	989	8e-05 (0.000392)	0.00056 (0.00214)	0.0636 (0.118)	0.561 (0.662)	0.198 (0.3)	0.0003 (0.00124)	0.369 (0.483)	0.0135 (0.0343)	0.483 (0.597)	0.326 (0.44)	0.122 (0.203)	0.0555 (0.107)
16p gain	54 (5%)	1036	0.00746 (0.0208)	0.0664 (0.122)	0.414 (0.534)	0.272 (0.383)	0.0219 (0.0517)	0.879 (0.915)	0.0481 (0.0959)	0.861 (0.899)	0.181 (0.279)	0.0199 (0.0478)	0.105 (0.179)	0.407 (0.526)
2p loss	54 (5%)	1036	0.0307 (0.0669)	0.0286 (0.064)	0.261 (0.371)	0.77 (0.83)	0.0578 (0.11)	0.0244 (0.0566)	0.198 (0.3)	0.0455 (0.092)	0.0714 (0.13)	0.4 (0.519)	0.492 (0.603)	0.2 (0.303)
2q loss	52 (5%)	1038	0.0348 (0.0741)	0.0137 (0.0345)	0.203 (0.305)	0.666 (0.75)	0.227 (0.332)	0.0181 (0.0441)	0.586 (0.684)	0.056 (0.108)	0.0329 (0.0706)	0.672 (0.753)	0.679 (0.76)	0.643 (0.732)
3q loss	64 (6%)	1026	0.222 (0.327)	0.206 (0.31)	0.595 (0.691)	0.841 (0.883)	0.532 (0.635)	0.152 (0.242)	0.0999 (0.172)	0.0354 (0.0751)	0.0472 (0.0945)	0.0129 (0.0329)	0.306 (0.418)	0.0306 (0.0669)
12q loss	109 (10%)	981	0.246 (0.354)	0.24 (0.348)	0.404 (0.524)	0.702 (0.779)	0.00558 (0.0161)	1e-05 (6.15e-05)	0.663 (0.75)	4e-05 (0.00021)	0.00904 (0.0246)	0.427 (0.546)	0.603 (0.699)	0.965 (0.983)
16p loss	78 (7%)	1012	0.285 (0.395)	0.852 (0.892)	0.663 (0.75)	0.736 (0.804)	1e-05 (6.15e-05)	0.00378 (0.0114)	0.00012 (0.000554)	0.00037 (0.00149)	0.933 (0.956)	0.465 (0.58)	0.514 (0.621)	0.0971 (0.169)
19p loss	57 (5%)	1033	0.00087 (0.00319)	0.00293 (0.0093)	0.0965 (0.168)	0.314 (0.426)	0.00961 (0.0258)	0.671 (0.753)	0.177 (0.275)	0.663 (0.75)	0.184 (0.283)	0.151 (0.242)	0.00555 (0.0161)	0.0533 (0.104)
20q loss	21 (2%)	1069	0.00146 (0.00494)	8e-05 (0.000392)	0.365 (0.481)	0.267 (0.377)	0.00545 (0.0159)	0.311 (0.423)	0.716 (0.789)	0.0123 (0.0319)	0.766 (0.827)	0.541 (0.643)	0.835 (0.88)	1 (1.00)
21q loss	79 (7%)	1011	0.0218 (0.0516)	0.00134 (0.00459)	0.054 (0.105)	0.264 (0.373)	0.069 (0.126)	4e-05 (0.00021)	0.18 (0.279)	2e-05 (0.000114)	0.33 (0.443)	0.0555 (0.107)	0.711 (0.786)	0.414 (0.534)
15q gain	36 (3%)	1054	0.0616 (0.115)	0.11 (0.187)	0.567 (0.664)	0.133 (0.217)	0.0599 (0.113)	0.0256 (0.0586)	0.0166 (0.0411)	0.00436 (0.013)	0.223 (0.328)	0.439 (0.557)	0.713 (0.786)	0.283 (0.393)
12p loss	86 (8%)	1004	0.213 (0.317)	0.246 (0.354)	0.557 (0.658)	0.789 (0.844)	0.0274 (0.0615)	0.0489 (0.0974)	0.248 (0.355)	0.0183 (0.0443)	0.0606 (0.114)	0.281 (0.393)	0.315 (0.427)	0.772 (0.831)
18p loss	137 (13%)	953	0.047 (0.0941)	0.0319 (0.0687)	0.361 (0.478)	0.22 (0.324)	0.562 (0.662)	0.0256 (0.0586)	0.904 (0.933)	0.622 (0.715)	0.456 (0.573)	0.874 (0.911)	0.406 (0.525)	0.503 (0.613)
20p loss	26 (2%)	1064	0.00016 (0.000709)	2e-05 (0.000114)	0.0363 (0.0765)	0.0938 (0.164)	0.0563 (0.108)	0.194 (0.295)	0.641 (0.732)	0.185 (0.284)	0.444 (0.562)	0.484 (0.597)	0.712 (0.786)	0.48 (0.595)
14q gain	26 (2%)	1064	0.431 (0.548)	0.78 (0.837)	0.0102 (0.0271)	0.807 (0.857)	0.0002 (0.000859)	0.483 (0.597)	0.105 (0.179)	0.0778 (0.139)	0.367 (0.481)	0.683 (0.761)	0.268 (0.378)	0.762 (0.824)
16q gain	56 (5%)	1034	0.0179 (0.0438)	0.00559 (0.0161)	0.358 (0.475)	0.0677 (0.124)	0.0564 (0.108)	0.343 (0.458)	0.36 (0.477)	0.462 (0.578)	0.0537 (0.105)	0.102 (0.176)	0.14 (0.228)	0.534 (0.636)
1q loss	44 (4%)	1046	0.829 (0.875)	0.977 (0.993)	0.857 (0.896)	0.362 (0.478)	0.21 (0.313)	0.0201 (0.0482)	0.208 (0.312)	0.0412 (0.0851)	0.212 (0.316)	0.368 (0.482)	0.24 (0.349)	0.161 (0.254)
18q loss	123 (11%)	967	0.181 (0.279)	0.00856 (0.0235)	0.64 (0.732)	0.327 (0.441)	0.509 (0.619)	0.00102 (0.00362)	1 (1.00)	0.291 (0.401)	0.058 (0.11)	0.71 (0.786)	0.419 (0.54)	0.53 (0.635)
10q gain	12 (1%)	1078	0.553 (0.655)	1 (1.00)	0.0519 (0.102)	0.794 (0.846)	0.0756 (0.136)	0.00156 (0.00526)	0.724 (0.795)	0.122 (0.203)	0.148 (0.238)	0.158 (0.251)	0.767 (0.828)	0.564 (0.663)
xp gain	35 (3%)	1055	0.281 (0.393)	1 (1.00)	0.795 (0.846)	0.185 (0.284)	0.691 (0.767)	0.00014 (0.000638)	0.458 (0.574)	0.735 (0.804)	0.62 (0.714)	0.911 (0.938)	0.917 (0.942)	0.492 (0.603)
7p loss	10 (1%)	1080	0.0304 (0.0669)	0.0898 (0.158)	0.215 (0.319)	0.0612 (0.115)	0.426 (0.546)	0.132 (0.215)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
13q gain	17 (2%)	1073	0.0525 (0.103)	0.493 (0.603)	0.18 (0.279)	0.824 (0.873)	0.851 (0.892)	0.335 (0.45)	0.259 (0.368)	0.53 (0.635)	0.291 (0.401)	0.428 (0.546)	0.273 (0.384)	0.499 (0.61)
7q loss	9 (1%)	1081	0.095 (0.166)	0.616 (0.711)	0.589 (0.686)	0.211 (0.315)	0.566 (0.664)	0.0867 (0.154)	0.685 (0.763)	1 (1.00)	1 (1.00)	0.83 (0.875)	0.206 (0.31)	1 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S1. Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
1P GAIN MUTATED	79	10	6
1P GAIN WILD-TYPE	454	532	9

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S2. Gene #1: '1p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
1P GAIN MUTATED	20	5	0	0
1P GAIN WILD-TYPE	164	232	64	165

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
1P GAIN MUTATED	36	3	0
1P GAIN WILD-TYPE	197	232	192

Figure S3. 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 = 6.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
1P GAIN MUTATED	33	6	0
1P GAIN WILD-TYPE	170	184	267

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
1P GAIN MUTATED	8	4	1	0
1P GAIN WILD-TYPE	129	103	182	82

Figure S5. 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 = 6.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
1P GAIN MUTATED	3	0	10
1P GAIN WILD-TYPE	219	184	93

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.032

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
1P GAIN MUTATED	10	1	2
1P GAIN WILD-TYPE	175	160	157

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00082

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
1P GAIN MUTATED	1	2	1	9
1P GAIN WILD-TYPE	90	135	187	80

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S9. Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
1Q GAIN MUTATED	83	23	6
1Q GAIN WILD-TYPE	450	519	9

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S10. Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
1Q GAIN MUTATED	26	9	1	2
1Q GAIN WILD-TYPE	158	228	63	163

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S11. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
1Q GAIN MUTATED	39	5	6
1Q GAIN WILD-TYPE	194	230	186

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S12. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
1Q GAIN MUTATED	35	9	6
1Q GAIN WILD-TYPE	168	181	261

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.067

Table S13. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
1Q GAIN MUTATED	7	6	10
1Q GAIN WILD-TYPE	215	178	93

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.067

Table S14. Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
1Q GAIN MUTATED	12	2	9
1Q GAIN WILD-TYPE	173	159	150

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0036

Table S15. Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
2P GAIN MUTATED	37	13	1
2P GAIN WILD-TYPE	496	529	14

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.0098

Table S16. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
2P GAIN MUTATED	17	5	3
2P GAIN WILD-TYPE	216	230	189

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.007

Table S17. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
2P GAIN MUTATED	16	4	5
2P GAIN WILD-TYPE	187	186	262

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.048

Table S18. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
2P GAIN MUTATED	5	2	7
2P GAIN WILD-TYPE	217	182	96

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.086

Table S19. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
2P GAIN MUTATED	1	5	2	6
2P GAIN WILD-TYPE	90	132	186	83

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MIR_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.098

Table S20. Gene #4: '2q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
2Q GAIN MUTATED	8	11	2	14
2Q GAIN WILD-TYPE	148	172	85	106

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

'2q gain' versus 'CN_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.011

Table S21. Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
2Q GAIN MUTATED	34	13	1
2Q GAIN WILD-TYPE	499	529	14

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.012

Table S22. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
2Q GAIN MUTATED	16	4	3
2Q GAIN WILD-TYPE	217	231	189

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0025

Table S23. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
2Q GAIN MUTATED	16	3	4
2Q GAIN WILD-TYPE	187	187	263

Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.043

Table S24. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
2Q GAIN MUTATED	4	2	7
2Q GAIN WILD-TYPE	218	182	96

Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.093

Table S25. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
2Q GAIN MUTATED	1	4	2	6
2Q GAIN WILD-TYPE	90	133	186	83

Figure S25. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00075

Table S26. Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
3P GAIN MUTATED	16	18	4	15
3P GAIN WILD-TYPE	131	78	148	98

Figure S26. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.032

Table S27. Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
3P GAIN MUTATED	13	18	4	18
3P GAIN WILD-TYPE	135	84	96	140

Figure S27. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.066

Table S28. Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
3P GAIN MUTATED	35	5	14
3P GAIN WILD-TYPE	258	119	115

Figure S28. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S29. Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
3P GAIN MUTATED	51	14	2
3P GAIN WILD-TYPE	482	528	13

Figure S29. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.061

Table S30. Gene #5: '3p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
3P GAIN MUTATED	13	5	1	3
3P GAIN WILD-TYPE	171	232	63	162

Figure S30. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0014

Table S31. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
3P GAIN MUTATED	21	5	3
3P GAIN WILD-TYPE	212	230	189

Figure S31. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00071

Table S32. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
3P GAIN MUTATED	19	6	4
3P GAIN WILD-TYPE	184	184	263

Figure S32. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00097

Table S33. Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
3Q GAIN MUTATED	17	21	6	15
3Q GAIN WILD-TYPE	130	75	146	98

Figure S33. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.074

Table S34. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
3Q GAIN MUTATED	14	19	6	20
3Q GAIN WILD-TYPE	134	83	94	138

Figure S34. 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 = 6.1e-05

Table S35. Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
3Q GAIN MUTATED	54	15	2
3Q GAIN WILD-TYPE	479	527	13

Figure S35. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0024

Table S36. Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
3Q GAIN MUTATED	15	3	1	2
3Q GAIN WILD-TYPE	169	234	63	163

Figure S36. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S37. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
3Q GAIN MUTATED	26	2	3
3Q GAIN WILD-TYPE	207	233	189

Figure S37. 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 = 6.1e-05

Table S38. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
3Q GAIN MUTATED	24	4	3
3Q GAIN WILD-TYPE	179	186	264

Figure S38. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.088

Table S39. Gene #7: '4p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
4P GAIN MUTATED	7	7	2	0
4P GAIN WILD-TYPE	177	230	62	165

Figure S39. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.009

Table S40. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
4P GAIN MUTATED	14	5	1
4P GAIN WILD-TYPE	219	230	191

Figure S40. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0012

Table S41. Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
4P GAIN MUTATED	13	6	1
4P GAIN WILD-TYPE	190	184	266

Figure S41. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.092

Table S42. Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
4P GAIN MUTATED	3	3	6
4P GAIN WILD-TYPE	219	181	97

Figure S42. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.065

Table S43. Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
4Q GAIN MUTATED	27	12	1
4Q GAIN WILD-TYPE	506	530	14

Figure S43. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00594 (Fisher's exact test), Q value = 0.017

Table S44. Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
4Q GAIN MUTATED	8	2	2	0
4Q GAIN WILD-TYPE	176	235	62	165

Figure S44. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S45. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
4Q GAIN MUTATED	13	0	1
4Q GAIN WILD-TYPE	220	235	191

Figure S45. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S46. Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
4Q GAIN MUTATED	12	1	1
4Q GAIN WILD-TYPE	191	189	266

Figure S46. 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 = 6.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
5P GAIN MUTATED	46	12	2
5P GAIN WILD-TYPE	487	530	13

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

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 0.016

Table S48. Gene #9: '5p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
5P GAIN MUTATED	9	4	3	0
5P GAIN WILD-TYPE	175	233	61	165

Figure S48. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S49. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
5P GAIN MUTATED	18	2	1
5P GAIN WILD-TYPE	215	233	191

Figure S49. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S50. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
5P GAIN MUTATED	17	3	1
5P GAIN WILD-TYPE	186	187	266

Figure S50. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.056

Table S51. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
5P GAIN MUTATED	5	5	1	0
5P GAIN WILD-TYPE	132	102	182	82

Figure S51. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.059

Table S52. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
5P GAIN MUTATED	3	2	6
5P GAIN WILD-TYPE	219	182	97

Figure S52. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.04

Table S53. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
5P GAIN MUTATED	1	3	1	6
5P GAIN WILD-TYPE	90	134	187	83

Figure S53. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S54. Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
5Q GAIN MUTATED	41	7	2
5Q GAIN WILD-TYPE	492	535	13

Figure S54. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0024

Table S55. Gene #10: '5q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
5Q GAIN MUTATED	10	2	3	0
5Q GAIN WILD-TYPE	174	235	61	165

Figure S55. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S56. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
5Q GAIN MUTATED	17	1	1
5Q GAIN WILD-TYPE	216	234	191

Figure S56. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S57. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
5Q GAIN MUTATED	17	1	1
5Q GAIN WILD-TYPE	186	189	266

Figure S57. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00586 (Fisher's exact test), Q value = 0.017

Table S58. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
5Q GAIN MUTATED	2	1	6
5Q GAIN WILD-TYPE	220	183	97

Figure S58. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.092

Table S59. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
5Q GAIN MUTATED	7	1	1
5Q GAIN WILD-TYPE	178	160	158

Figure S59. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00501 (Fisher's exact test), Q value = 0.015

Table S60. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
5Q GAIN MUTATED	1	1	1	6
5Q GAIN WILD-TYPE	90	136	187	83

Figure S60. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.038

Table S61. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
6P GAIN MUTATED	4	10	3	4
6P GAIN WILD-TYPE	143	86	149	109

Figure S61. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.052

Table S62. Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
6P GAIN MUTATED	6	9	0	0
6P GAIN WILD-TYPE	178	228	64	165

Figure S62. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.03

Table S63. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
6P GAIN MUTATED	4	5	0	1
6P GAIN WILD-TYPE	133	102	183	81

Figure S63. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.054

Table S64. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
6P GAIN MUTATED	6	0	4
6P GAIN WILD-TYPE	216	184	99

Figure S64. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0056

Table S65. Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
6Q GAIN MUTATED	4	11	2	3
6Q GAIN WILD-TYPE	143	85	150	110

Figure S65. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.077

Table S66. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
6Q GAIN MUTATED	5	7	0	8
6Q GAIN WILD-TYPE	143	95	100	150

Figure S66. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.066

Table S67. Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
6Q GAIN MUTATED	16	10	2
6Q GAIN WILD-TYPE	517	532	13

Figure S67. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.017

Table S68. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
6Q GAIN MUTATED	0	4	0	1
6Q GAIN WILD-TYPE	137	103	183	81

Figure S68. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S69. Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
7P GAIN MUTATED	135	65	129	83
7P GAIN WILD-TYPE	12	31	23	30

Figure S69. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S70. Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
7P GAIN MUTATED	132	55	86	139
7P GAIN WILD-TYPE	16	47	14	19

Figure S70. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0026

Table S71. Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
7P GAIN MUTATED	139	137	65	105
7P GAIN WILD-TYPE	17	46	22	15

Figure S71. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S72. Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
7P GAIN MUTATED	215	113	118
7P GAIN WILD-TYPE	78	11	11

Figure S72. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S73. Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
7P GAIN MUTATED	479	106	10
7P GAIN WILD-TYPE	54	436	5

Figure S73. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S74. Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
7P GAIN MUTATED	155	47	23	15
7P GAIN WILD-TYPE	29	190	41	150

Figure S74. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S75. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
7P GAIN MUTATED	168	39	38
7P GAIN WILD-TYPE	65	196	154

Figure S75. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S76. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
7P GAIN MUTATED	166	31	48
7P GAIN WILD-TYPE	37	159	219

Figure S76. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.0091

Table S77. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
7P GAIN MUTATED	43	34	32	14
7P GAIN WILD-TYPE	94	73	151	68

Figure S77. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S78. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
7P GAIN MUTATED	40	28	55
7P GAIN WILD-TYPE	182	156	48

Figure S78. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00097

Table S79. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
7P GAIN MUTATED	63	25	34
7P GAIN WILD-TYPE	122	136	125

Figure S79. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S80. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
7P GAIN MUTATED	14	22	35	51
7P GAIN WILD-TYPE	77	115	153	38

Figure S80. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S81. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
7Q GAIN MUTATED	135	62	130	88
7Q GAIN WILD-TYPE	12	34	22	25

Figure S81. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S82. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
7Q GAIN MUTATED	130	61	85	139
7Q GAIN WILD-TYPE	18	41	15	19

Figure S82. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'MIR_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0072

Table S83. Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
7Q GAIN MUTATED	140	137	69	103
7Q GAIN WILD-TYPE	16	46	18	17

Figure S83. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S84. Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
7Q GAIN MUTATED	222	112	115
7Q GAIN WILD-TYPE	71	12	14

Figure S84. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S85. Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
7Q GAIN MUTATED	484	137	10
7Q GAIN WILD-TYPE	49	405	5

Figure S85. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S86. Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
7Q GAIN MUTATED	160	65	26	23
7Q GAIN WILD-TYPE	24	172	38	142

Figure S86. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S87. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
7Q GAIN MUTATED	174	53	52
7Q GAIN WILD-TYPE	59	182	140

Figure S87. 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 = 6.1e-05

Table S88. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
7Q GAIN MUTATED	171	43	65
7Q GAIN WILD-TYPE	32	147	202

Figure S88. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00842 (Fisher's exact test), Q value = 0.023

Table S89. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
7Q GAIN MUTATED	49	41	47	16
7Q GAIN WILD-TYPE	88	66	136	66

Figure S89. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S90. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
7Q GAIN MUTATED	51	43	59
7Q GAIN WILD-TYPE	171	141	44

Figure S90. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0034

Table S91. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
7Q GAIN MUTATED	71	32	49
7Q GAIN WILD-TYPE	114	129	110

Figure S91. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S92. Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
7Q GAIN MUTATED	19	29	49	55
7Q GAIN WILD-TYPE	72	108	139	34

Figure S92. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S93. Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
8P GAIN MUTATED	7	18	6	17
8P GAIN WILD-TYPE	140	78	146	96

Figure S93. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0021

Table S94. Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
8P GAIN MUTATED	10	21	4	13
8P GAIN WILD-TYPE	138	81	96	145

Figure S94. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0012

Table S95. Gene #15: '8p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
8P GAIN MUTATED	10	37	3	8
8P GAIN WILD-TYPE	174	200	61	157

Figure S95. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
8P GAIN MUTATED	20	29	18
8P GAIN WILD-TYPE	183	161	249

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

'8q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S97. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
8Q GAIN MUTATED	7	20	7	20
8Q GAIN WILD-TYPE	140	76	145	93

Figure S97. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S98. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
8Q GAIN MUTATED	9	26	4	15
8Q GAIN WILD-TYPE	139	76	96	143

Figure S98. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'MIR_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.082

Table S99. Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
8Q GAIN MUTATED	10	27	10	8
8Q GAIN WILD-TYPE	146	156	77	112

Figure S99. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.046

Table S100. Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
8Q GAIN MUTATED	44	72	2
8Q GAIN WILD-TYPE	489	470	13

Figure S100. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S101. Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
8Q GAIN MUTATED	11	46	4	8
8Q GAIN WILD-TYPE	173	191	60	157

Figure S101. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
8Q GAIN MUTATED	21	37	21
8Q GAIN WILD-TYPE	182	153	246

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

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.073

Table S103. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
8Q GAIN MUTATED	25	23	10
8Q GAIN WILD-TYPE	160	138	149

Figure S103. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.029

Table S104. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
8Q GAIN MUTATED	20	13	19	6
8Q GAIN WILD-TYPE	71	124	169	83

Figure S104. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.011

Table S105. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
9P GAIN MUTATED	14	17	7	6
9P GAIN WILD-TYPE	133	79	145	107

Figure S105. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.067

Table S106. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
9P GAIN MUTATED	15	12	2	15
9P GAIN WILD-TYPE	133	90	98	143

Figure S106. 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 = 6.1e-05

Table S107. Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
9P GAIN MUTATED	44	16	4
9P GAIN WILD-TYPE	489	526	11

Figure S107. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.044

Table S108. Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
9P GAIN MUTATED	14	10	1	2
9P GAIN WILD-TYPE	170	227	63	163

Figure S108. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0019

Table S109. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
9P GAIN MUTATED	23	7	4
9P GAIN WILD-TYPE	210	228	188

Figure S109. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0017

Table S110. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
9P GAIN MUTATED	21	7	6
9P GAIN WILD-TYPE	182	183	261

Figure S110. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.061

Table S111. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
9P GAIN MUTATED	4	5	8
9P GAIN WILD-TYPE	218	179	95

Figure S111. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MRNA_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.098

Table S112. Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
9Q GAIN MUTATED	20	20	13	13
9Q GAIN WILD-TYPE	127	76	139	100

Figure S112. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S113. Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
9Q GAIN MUTATED	64	28	4
9Q GAIN WILD-TYPE	469	514	11

Figure S113. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.035

Table S114. Gene #18: '9q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
9Q GAIN MUTATED	17	16	2	3
9Q GAIN WILD-TYPE	167	221	62	162

Figure S114. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00064

Table S115. Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
9Q GAIN MUTATED	28	10	5
9Q GAIN WILD-TYPE	205	225	187

Figure S115. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.0097

Table S116. Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
9Q GAIN MUTATED	23	11	9
9Q GAIN WILD-TYPE	180	179	258

Figure S116. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.028

Table S117. Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
9Q GAIN MUTATED	6	7	11
9Q GAIN WILD-TYPE	216	177	92

Figure S117. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MRNA_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0036

Table S118. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
10P GAIN MUTATED	1	6	0	5
10P GAIN WILD-TYPE	146	90	152	108

Figure S118. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S119. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
10P GAIN MUTATED	2	9	0	1
10P GAIN WILD-TYPE	146	93	100	157

Figure S119. 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 = 6.1e-05

Table S120. Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
10P GAIN MUTATED	2	68	0
10P GAIN WILD-TYPE	531	474	15

Figure S120. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S121. Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
10P GAIN MUTATED	0	56	2	0
10P GAIN WILD-TYPE	184	181	62	165

Figure S121. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S122. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
10P GAIN MUTATED	8	38	13
10P GAIN WILD-TYPE	225	197	179

Figure S122. 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 = 6.1e-05

Table S123. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
10P GAIN MUTATED	2	43	14
10P GAIN WILD-TYPE	201	147	253

Figure S123. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.014

Table S124. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
10P GAIN MUTATED	20	15	14	7
10P GAIN WILD-TYPE	71	122	174	82

Figure S124. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0053

Table S125. Gene #20: '10q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
10Q GAIN MUTATED	0	9	0	0
10Q GAIN WILD-TYPE	184	228	64	165

Figure S125. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.034

Table S126. Gene #21: '11p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
11P GAIN MUTATED	15	35	0
11P GAIN WILD-TYPE	518	507	15

Figure S126. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S127. Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
11P GAIN MUTATED	3	12	1	20
11P GAIN WILD-TYPE	181	225	63	145

Figure S127. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.031

Table S128. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
11P GAIN MUTATED	6	9	25
11P GAIN WILD-TYPE	197	181	242

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

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.03

Table S129. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11P GAIN MUTATED	15	17	1
11P GAIN WILD-TYPE	207	167	102

Figure S129. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.011

Table S130. Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11P GAIN MUTATED	4	10	19	0
11P GAIN WILD-TYPE	87	127	169	89

Figure S130. 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 = 6.1e-05

Table S131. Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
11Q GAIN MUTATED	11	63	0
11Q GAIN WILD-TYPE	522	479	15

Figure S131. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
11Q GAIN MUTATED	4	32	1	24
11Q GAIN WILD-TYPE	180	205	63	141

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

'11q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
11Q GAIN MUTATED	7	35	20
11Q GAIN WILD-TYPE	226	200	172

Figure S133. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S134. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
11Q GAIN MUTATED	3	23	36
11Q GAIN WILD-TYPE	200	167	231

Figure S134. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.08

Table S135. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11Q GAIN MUTATED	31	23	5
11Q GAIN WILD-TYPE	191	161	98

Figure S135. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0315 (Fisher's exact test), Q value = 0.068

Table S136. Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11Q GAIN MUTATED	11	18	27	3
11Q GAIN WILD-TYPE	80	119	161	86

Figure S136. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.0088

Table S137. Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
12P GAIN MUTATED	15	25	1	4
12P GAIN WILD-TYPE	169	212	63	161

Figure S137. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.013

Table S138. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
12P GAIN MUTATED	23	21	5
12P GAIN WILD-TYPE	210	214	187

Figure S138. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.048

Table S139. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
12P GAIN MUTATED	21	17	11
12P GAIN WILD-TYPE	182	173	256

Figure S139. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.069

Table S140. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
12P GAIN MUTATED	12	11	5	6
12P GAIN WILD-TYPE	125	96	178	76

Figure S140. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00784 (Fisher's exact test), Q value = 0.022

Table S141. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
12P GAIN MUTATED	17	5	12
12P GAIN WILD-TYPE	205	179	91

Figure S141. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.027

Table S142. Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
12Q GAIN MUTATED	16	15	17
12Q GAIN WILD-TYPE	277	109	112

Figure S142. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S143. Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
12Q GAIN MUTATED	49	17	0
12Q GAIN WILD-TYPE	484	525	15

Figure S143. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.083

Table S144. Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
12Q GAIN MUTATED	14	9	1	3
12Q GAIN WILD-TYPE	170	228	63	162

Figure S144. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.004

Table S145. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
12Q GAIN MUTATED	19	8	2
12Q GAIN WILD-TYPE	214	227	190

Figure S145. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0044

Table S146. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
12Q GAIN MUTATED	18	6	5
12Q GAIN WILD-TYPE	185	184	262

Figure S146. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.046

Table S147. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
12Q GAIN MUTATED	7	4	1	5
12Q GAIN WILD-TYPE	130	103	182	77

Figure S147. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.012

Table S148. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
12Q GAIN MUTATED	6	2	9
12Q GAIN WILD-TYPE	216	182	94

Figure S148. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIR_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.027

Table S149. Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
14Q GAIN MUTATED	10	4	7	1
14Q GAIN WILD-TYPE	146	179	80	119

Figure S149. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00086

Table S150. Gene #26: '14q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
14Q GAIN MUTATED	20	4	2
14Q GAIN WILD-TYPE	513	538	13

Figure S150. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.059

Table S151. Gene #27: '15q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
15Q GAIN MUTATED	5	9	0	0
15Q GAIN WILD-TYPE	179	228	64	165

Figure S151. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.041

Table S152. Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
15Q GAIN MUTATED	13	5	2
15Q GAIN WILD-TYPE	220	230	190

Figure S152. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00436 (Fisher's exact test), Q value = 0.013

Table S153. Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
15Q GAIN MUTATED	12	6	2
15Q GAIN WILD-TYPE	191	184	265

Figure S153. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00746 (Fisher's exact test), Q value = 0.021

Table S154. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
16P GAIN MUTATED	12	11	3	11
16P GAIN WILD-TYPE	135	85	149	102

Figure S154. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.052

Table S155. Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
16P GAIN MUTATED	30	21	3
16P GAIN WILD-TYPE	503	521	12

Figure S155. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.096

Table S156. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
16P GAIN MUTATED	12	3	8
16P GAIN WILD-TYPE	221	232	184

Figure S156. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.048

Table S157. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
16P GAIN MUTATED	2	10	4
16P GAIN WILD-TYPE	220	174	99

Figure S157. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.044

Table S158. Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
16Q GAIN MUTATED	10	12	4	10
16Q GAIN WILD-TYPE	137	84	148	103

Figure S158. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.016

Table S159. Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
16Q GAIN MUTATED	10	15	2	9
16Q GAIN WILD-TYPE	138	87	98	149

Figure S159. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00068

Table S160. Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
17P GAIN MUTATED	9	15	4	16
17P GAIN WILD-TYPE	138	81	148	97

Figure S160. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.028

Table S161. Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
17P GAIN MUTATED	9	17	4	14
17P GAIN WILD-TYPE	139	85	96	144

Figure S161. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.048

Table S162. Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
17P GAIN MUTATED	34	8	5
17P GAIN WILD-TYPE	259	116	124

Figure S162. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0057

Table S163. Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
17P GAIN MUTATED	48	22	2
17P GAIN WILD-TYPE	485	520	13

Figure S163. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.083

Table S164. Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
17P GAIN MUTATED	17	12	4
17P GAIN WILD-TYPE	216	223	188

Figure S164. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.004

Table S165. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
17Q GAIN MUTATED	13	17	6	17
17Q GAIN WILD-TYPE	134	79	146	96

Figure S165. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.094

Table S166. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
17Q GAIN MUTATED	11	17	6	19
17Q GAIN WILD-TYPE	137	85	94	139

Figure S166. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.068

Table S167. Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
17Q GAIN MUTATED	40	9	8
17Q GAIN WILD-TYPE	253	115	121

Figure S167. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00043

Table S168. Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
17Q GAIN MUTATED	58	25	3
17Q GAIN WILD-TYPE	475	517	12

Figure S168. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0059

Table S169. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
17Q GAIN MUTATED	24	15	4
17Q GAIN WILD-TYPE	209	220	188

Figure S169. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.063

Table S170. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
17Q GAIN MUTATED	21	11	11
17Q GAIN WILD-TYPE	182	179	256

Figure S170. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.06

Table S171. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
17Q GAIN MUTATED	6	11	4	5
17Q GAIN WILD-TYPE	131	96	179	77

Figure S171. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S172. Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
18P GAIN MUTATED	10	25	5	15
18P GAIN WILD-TYPE	137	71	147	98

Figure S172. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0018

Table S173. Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
18P GAIN MUTATED	11	22	4	18
18P GAIN WILD-TYPE	137	80	96	140

Figure S173. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.0073

Table S174. Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
18P GAIN MUTATED	46	28	4
18P GAIN WILD-TYPE	487	514	11

Figure S174. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.041

Table S175. Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
18P GAIN MUTATED	11	14	2	1
18P GAIN WILD-TYPE	173	223	62	164

Figure S175. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S176. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
18P GAIN MUTATED	26	7	4
18P GAIN WILD-TYPE	207	228	188

Figure S176. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0016

Table S177. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
18P GAIN MUTATED	21	11	5
18P GAIN WILD-TYPE	182	179	262

Figure S177. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.075

Table S178. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
18P GAIN MUTATED	2	8	3	7
18P GAIN WILD-TYPE	89	129	185	82

Figure S178. 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 = 6.1e-05

Table S179. Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
18Q GAIN MUTATED	9	24	6	17
18Q GAIN WILD-TYPE	138	72	146	96

Figure S179. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0014

Table S180. Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
18Q GAIN MUTATED	10	24	6	16
18Q GAIN WILD-TYPE	138	78	94	142

Figure S180. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00071

Table S181. Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
18Q GAIN MUTATED	49	22	4
18Q GAIN WILD-TYPE	484	520	11

Figure S181. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0033

Table S182. Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
18Q GAIN MUTATED	14	10	2	0
18Q GAIN WILD-TYPE	170	227	62	165

Figure S182. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S183. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
18Q GAIN MUTATED	28	5	1
18Q GAIN WILD-TYPE	205	230	191

Figure S183. 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 = 6.1e-05

Table S184. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
18Q GAIN MUTATED	23	9	2
18Q GAIN WILD-TYPE	180	181	265

Figure S184. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00897 (Fisher's exact test), Q value = 0.024

Table S185. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
18Q GAIN MUTATED	6	2	8
18Q GAIN WILD-TYPE	216	182	95

Figure S185. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0039

Table S186. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
18Q GAIN MUTATED	1	6	1	8
18Q GAIN WILD-TYPE	90	131	187	81

Figure S186. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S187. Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
19P GAIN MUTATED	52	34	91	20
19P GAIN WILD-TYPE	95	62	61	93

Figure S187. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S188. Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
19P GAIN MUTATED	62	25	58	52
19P GAIN WILD-TYPE	86	77	42	106

Figure S188. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0015

Table S189. Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
19P GAIN MUTATED	94	49	68
19P GAIN WILD-TYPE	199	75	61

Figure S189. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S190. Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
19P GAIN MUTATED	235	82	6
19P GAIN WILD-TYPE	298	460	9

Figure S190. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S191. Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
19P GAIN MUTATED	72	12	6	57
19P GAIN WILD-TYPE	112	225	58	108

Figure S191. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S192. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
19P GAIN MUTATED	77	31	39
19P GAIN WILD-TYPE	156	204	153

Figure S192. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S193. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
19P GAIN MUTATED	72	12	63
19P GAIN WILD-TYPE	131	178	204

Figure S193. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0046

Table S194. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
19P GAIN MUTATED	19	17	33	29
19P GAIN WILD-TYPE	118	90	150	53

Figure S194. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.068

Table S195. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
19P GAIN MUTATED	33	37	28
19P GAIN WILD-TYPE	189	147	75

Figure S195. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.022

Table S196. Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
19P GAIN MUTATED	9	30	33	26
19P GAIN WILD-TYPE	82	107	155	63

Figure S196. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S197. Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
19Q GAIN MUTATED	46	27	83	14
19Q GAIN WILD-TYPE	101	69	69	99

Figure S197. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S198. Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
19Q GAIN MUTATED	55	18	54	43
19Q GAIN WILD-TYPE	93	84	46	115

Figure S198. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00974 (Fisher's exact test), Q value = 0.026

Table S199. Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
19Q GAIN MUTATED	82	45	55
19Q GAIN WILD-TYPE	211	79	74

Figure S199. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S200. Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
19Q GAIN MUTATED	204	12	6
19Q GAIN WILD-TYPE	329	530	9

Figure S200. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S201. Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
19Q GAIN MUTATED	59	3	5	0
19Q GAIN WILD-TYPE	125	234	59	165

Figure S201. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S202. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
19Q GAIN MUTATED	66	1	5
19Q GAIN WILD-TYPE	167	234	187

Figure S202. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S203. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
19Q GAIN MUTATED	64	4	4
19Q GAIN WILD-TYPE	139	186	263

Figure S203. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.004

Table S204. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
19Q GAIN MUTATED	8	13	6	0
19Q GAIN WILD-TYPE	129	94	177	82

Figure S204. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S205. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
19Q GAIN MUTATED	4	2	21
19Q GAIN WILD-TYPE	218	182	82

Figure S205. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S206. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
19Q GAIN MUTATED	21	1	5
19Q GAIN WILD-TYPE	164	160	154

Figure S206. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S207. Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
19Q GAIN MUTATED	3	0	2	22
19Q GAIN WILD-TYPE	88	137	186	67

Figure S207. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S208. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
20P GAIN MUTATED	51	26	86	29
20P GAIN WILD-TYPE	96	70	66	84

Figure S208. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S209. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
20P GAIN MUTATED	55	21	64	52
20P GAIN WILD-TYPE	93	81	36	106

Figure S209. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.013

Table S210. Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
20P GAIN MUTATED	61	75	20	56
20P GAIN WILD-TYPE	95	108	67	64

Figure S210. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S211. Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
20P GAIN MUTATED	85	58	69
20P GAIN WILD-TYPE	208	66	60

Figure S211. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S212. Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
20P GAIN MUTATED	224	39	3
20P GAIN WILD-TYPE	309	503	12

Figure S212. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S213. Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
20P GAIN MUTATED	69	9	5	7
20P GAIN WILD-TYPE	115	228	59	158

Figure S213. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S214. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
20P GAIN MUTATED	75	8	14
20P GAIN WILD-TYPE	158	227	178

Figure S214. 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 = 6.1e-05

Table S215. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
20P GAIN MUTATED	73	9	15
20P GAIN WILD-TYPE	130	181	252

Figure S215. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S216. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
20P GAIN MUTATED	8	10	26
20P GAIN WILD-TYPE	214	174	77

Figure S216. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0085

Table S217. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
20P GAIN MUTATED	26	6	12
20P GAIN WILD-TYPE	159	155	147

Figure S217. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S218. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
20P GAIN MUTATED	3	5	10	26
20P GAIN WILD-TYPE	88	132	178	63

Figure S218. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S219. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
20Q GAIN MUTATED	50	28	86	27
20Q GAIN WILD-TYPE	97	68	66	86

Figure S219. 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 = 6.1e-05

Table S220. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
20Q GAIN MUTATED	58	22	62	49
20Q GAIN WILD-TYPE	90	80	38	109

Figure S220. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.0094

Table S221. Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
20Q GAIN MUTATED	62	74	19	55
20Q GAIN WILD-TYPE	94	109	68	65

Figure S221. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S222. Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
20Q GAIN MUTATED	85	57	68
20Q GAIN WILD-TYPE	208	67	61

Figure S222. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S223. Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
20Q GAIN MUTATED	223	37	3
20Q GAIN WILD-TYPE	310	505	12

Figure S223. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S224. Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
20Q GAIN MUTATED	70	8	5	6
20Q GAIN WILD-TYPE	114	229	59	159

Figure S224. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S225. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
20Q GAIN MUTATED	77	7	12
20Q GAIN WILD-TYPE	156	228	180

Figure S225. 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 = 6.1e-05

Table S226. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
20Q GAIN MUTATED	74	9	13
20Q GAIN WILD-TYPE	129	181	254

Figure S226. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.058

Table S227. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
20Q GAIN MUTATED	17	13	10	3
20Q GAIN WILD-TYPE	120	94	173	79

Figure S227. 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 = 6.1e-05

Table S228. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
20Q GAIN MUTATED	9	8	26
20Q GAIN WILD-TYPE	213	176	77

Figure S228. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00071

Table S229. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
20Q GAIN MUTATED	28	5	10
20Q GAIN WILD-TYPE	157	156	149

Figure S229. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S230. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
20Q GAIN MUTATED	6	4	7	26
20Q GAIN WILD-TYPE	85	133	181	63

Figure S230. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0046

Table S231. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
21Q GAIN MUTATED	28	11	9	7
21Q GAIN WILD-TYPE	119	85	143	106

Figure S231. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00734 (Fisher's exact test), Q value = 0.021

Table S232. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
21Q GAIN MUTATED	25	6	5	19
21Q GAIN WILD-TYPE	123	96	95	139

Figure S232. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'MIR_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.029

Table S233. Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
21Q GAIN MUTATED	24	15	4	19
21Q GAIN WILD-TYPE	132	168	83	101

Figure S233. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'21q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.011

Table S234. Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
21Q GAIN MUTATED	26	25	11
21Q GAIN WILD-TYPE	267	99	118

Figure S234. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S235. Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
21Q GAIN MUTATED	63	24	1
21Q GAIN WILD-TYPE	470	518	14

Figure S235. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.049

Table S236. Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
21Q GAIN MUTATED	17	6	2	9
21Q GAIN WILD-TYPE	167	231	62	156

Figure S236. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 9e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
21Q GAIN MUTATED	30	8	9
21Q GAIN WILD-TYPE	203	227	183

Figure S237. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S238. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
21Q GAIN MUTATED	30	5	12
21Q GAIN WILD-TYPE	173	185	255

Figure S238. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S239. Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
22Q GAIN MUTATED	5	14	0	10
22Q GAIN WILD-TYPE	142	82	152	103

Figure S239. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00656 (Fisher's exact test), Q value = 0.019

Table S240. Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
22Q GAIN MUTATED	10	10	0	9
22Q GAIN WILD-TYPE	138	92	100	149

Figure S240. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S241. Gene #39: '22q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
22Q GAIN MUTATED	7	2	0	18
22Q GAIN WILD-TYPE	177	235	64	147

Figure S241. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.034

Table S242. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
22Q GAIN MUTATED	13	3	19
22Q GAIN WILD-TYPE	190	187	248

Figure S242. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.087

Table S243. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
22Q GAIN MUTATED	3	10	10
22Q GAIN WILD-TYPE	182	151	149

Figure S243. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00064

Table S244. Gene #40: 'xp gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
XP GAIN MUTATED	5	18	0	0
XP GAIN WILD-TYPE	179	219	64	165

Figure S244. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.0097

Table S245. Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
XQ GAIN MUTATED	17	42	0
XQ GAIN WILD-TYPE	516	500	15

Figure S245. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S246. Gene #41: 'xq gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
XQ GAIN MUTATED	6	36	3	0
XQ GAIN WILD-TYPE	178	201	61	165

Figure S246. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.088

Table S247. Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
XQ GAIN MUTATED	11	25	12
XQ GAIN WILD-TYPE	222	210	180

Figure S247. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0023

Table S248. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
XQ GAIN MUTATED	9	26	13
XQ GAIN WILD-TYPE	194	164	254

Figure S248. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.052

Table S249. Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
XQ GAIN MUTATED	15	7	14	5
XQ GAIN WILD-TYPE	76	130	174	84

Figure S249. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S250. Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
1P LOSS MUTATED	16	183	0
1P LOSS WILD-TYPE	517	359	15

Figure S250. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S251. Gene #42: '1p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
1P LOSS MUTATED	7	6	13	161
1P LOSS WILD-TYPE	177	231	51	4

Figure S251. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S252. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
1P LOSS MUTATED	10	80	97
1P LOSS WILD-TYPE	223	155	95

Figure S252. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S253. Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
1P LOSS MUTATED	6	11	170
1P LOSS WILD-TYPE	197	179	97

Figure S253. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S254. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
1P LOSS MUTATED	26	9	83	65
1P LOSS WILD-TYPE	111	98	100	17

Figure S254. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S255. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
1P LOSS MUTATED	80	96	7
1P LOSS WILD-TYPE	142	88	96

Figure S255. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S256. Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
1P LOSS MUTATED	30	81	72
1P LOSS WILD-TYPE	155	80	87

Figure S256. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S257. Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
1P LOSS MUTATED	7	81	88	7
1P LOSS WILD-TYPE	84	56	100	82

Figure S257. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.048

Table S258. Gene #43: '1q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
1Q LOSS MUTATED	6	7	5	15
1Q LOSS WILD-TYPE	178	230	59	150

Figure S258. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.085

Table S259. Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
1Q LOSS MUTATED	6	7	21
1Q LOSS WILD-TYPE	197	183	246

Figure S259. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.067

Table S260. Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
2P LOSS MUTATED	7	12	5	5
2P LOSS WILD-TYPE	140	84	147	108

Figure S260. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.064

Table S261. Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
2P LOSS MUTATED	8	12	2	7
2P LOSS WILD-TYPE	140	90	98	151

Figure S261. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.057

Table S262. Gene #44: '2p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
2P LOSS MUTATED	11	17	2	2
2P LOSS WILD-TYPE	173	220	62	163

Figure S262. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.092

Table S263. Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
2P LOSS MUTATED	10	13	6
2P LOSS WILD-TYPE	193	177	261

Figure S263. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.074

Table S264. Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
2Q LOSS MUTATED	7	12	5	6
2Q LOSS WILD-TYPE	140	84	147	107

Figure S264. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.034

Table S265. Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
2Q LOSS MUTATED	8	13	2	7
2Q LOSS WILD-TYPE	140	89	98	151

Figure S265. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.044

Table S266. Gene #45: '2q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
2Q LOSS MUTATED	9	17	1	2
2Q LOSS WILD-TYPE	175	220	63	163

Figure S266. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.071

Table S267. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
2Q LOSS MUTATED	4	9	3	2
2Q LOSS WILD-TYPE	133	98	180	80

Figure S267. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.06

Table S268. Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
3P LOSS MUTATED	20	15	5
3P LOSS WILD-TYPE	213	220	187

Figure S268. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.088

Table S269. Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
3P LOSS MUTATED	17	14	9
3P LOSS WILD-TYPE	186	176	258

Figure S269. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0034

Table S270. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
3P LOSS MUTATED	9	14	3	4
3P LOSS WILD-TYPE	128	93	180	78

Figure S270. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0018

Table S271. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
3P LOSS MUTATED	18	2	10
3P LOSS WILD-TYPE	204	182	93

Figure S271. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.0091

Table S272. Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
3P LOSS MUTATED	11	6	4	8
3P LOSS WILD-TYPE	80	131	184	81

Figure S272. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.075

Table S273. Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
3Q LOSS MUTATED	12	16	8
3Q LOSS WILD-TYPE	191	174	259

Figure S273. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.094

Table S274. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
3Q LOSS MUTATED	8	12	6	3
3Q LOSS WILD-TYPE	129	95	177	79

Figure S274. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.033

Table S275. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
3Q LOSS MUTATED	15	4	10
3Q LOSS WILD-TYPE	207	180	93

Figure S275. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.067

Table S276. Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
3Q LOSS MUTATED	9	9	4	6
3Q LOSS WILD-TYPE	82	128	184	83

Figure S276. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.092

Table S277. Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
4P LOSS MUTATED	11	17	11	12
4P LOSS WILD-TYPE	136	79	141	101

Figure S277. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0055

Table S278. Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
4P LOSS MUTATED	10	20	4	17
4P LOSS WILD-TYPE	138	82	96	141

Figure S278. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.04

Table S279. Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
4P LOSS MUTATED	48	76	3
4P LOSS WILD-TYPE	485	466	12

Figure S279. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S280. Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
4P LOSS MUTATED	13	25	0	45
4P LOSS WILD-TYPE	171	212	64	120

Figure S280. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0059

Table S281. Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
4P LOSS MUTATED	20	19	53
4P LOSS WILD-TYPE	183	171	214

Figure S281. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S282. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
4P LOSS MUTATED	11	12	22	26
4P LOSS WILD-TYPE	126	95	161	56

Figure S282. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00094

Table S283. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
4P LOSS MUTATED	38	30	3
4P LOSS WILD-TYPE	184	154	100

Figure S283. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S284. Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
4P LOSS MUTATED	10	35	26
4P LOSS WILD-TYPE	175	126	133

Figure S284. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S285. Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
4P LOSS MUTATED	6	34	29	2
4P LOSS WILD-TYPE	85	103	159	87

Figure S285. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0011

Table S286. Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
4Q LOSS MUTATED	10	21	7	13
4Q LOSS WILD-TYPE	137	75	145	100

Figure S286. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00079

Table S287. Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
4Q LOSS MUTATED	10	22	3	16
4Q LOSS WILD-TYPE	138	80	97	142

Figure S287. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'MIR_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.067

Table S288. Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
4Q LOSS MUTATED	7	25	9	13
4Q LOSS WILD-TYPE	149	158	78	107

Figure S288. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S289. Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
4Q LOSS MUTATED	46	102	3
4Q LOSS WILD-TYPE	487	440	12

Figure S289. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S290. Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
4Q LOSS MUTATED	14	44	3	48
4Q LOSS WILD-TYPE	170	193	61	117

Figure S290. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00931 (Fisher's exact test), Q value = 0.025

Table S291. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
4Q LOSS MUTATED	27	51	37
4Q LOSS WILD-TYPE	206	184	155

Figure S291. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S292. Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
4Q LOSS MUTATED	20	30	65
4Q LOSS WILD-TYPE	183	160	202

Figure S292. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00064

Table S293. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
4Q LOSS MUTATED	12	19	35	27
4Q LOSS WILD-TYPE	125	88	148	55

Figure S293. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.012

Table S294. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
4Q LOSS MUTATED	44	41	8
4Q LOSS WILD-TYPE	178	143	95

Figure S294. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S295. Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
4Q LOSS MUTATED	14	43	36
4Q LOSS WILD-TYPE	171	118	123

Figure S295. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S296. Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
4Q LOSS MUTATED	9	39	39	6
4Q LOSS WILD-TYPE	82	98	149	83

Figure S296. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S297. Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
5P LOSS MUTATED	5	21	6	9
5P LOSS WILD-TYPE	142	75	146	104

Figure S297. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S298. Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
5P LOSS MUTATED	6	23	5	7
5P LOSS WILD-TYPE	142	79	95	151

Figure S298. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'MIR_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0026

Table S299. Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
5P LOSS MUTATED	4	25	6	6
5P LOSS WILD-TYPE	152	158	81	114

Figure S299. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0015

Table S300. Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
5P LOSS MUTATED	25	50	4
5P LOSS WILD-TYPE	508	492	11

Figure S300. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S301. Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
5P LOSS MUTATED	12	29	2	2
5P LOSS WILD-TYPE	172	208	62	163

Figure S301. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.089

Table S302. Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
5P LOSS MUTATED	14	22	14
5P LOSS WILD-TYPE	189	168	253

Figure S302. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S303. Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
5Q LOSS MUTATED	6	20	5	11
5Q LOSS WILD-TYPE	141	76	147	102

Figure S303. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S304. Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
5Q LOSS MUTATED	9	22	4	7
5Q LOSS WILD-TYPE	139	80	96	151

Figure S304. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'MIR_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0021

Table S305. Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
5Q LOSS MUTATED	4	26	6	6
5Q LOSS WILD-TYPE	152	157	81	114

Figure S305. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0028

Table S306. Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
5Q LOSS MUTATED	25	49	4
5Q LOSS WILD-TYPE	508	493	11

Figure S306. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0012

Table S307. Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
5Q LOSS MUTATED	12	27	2	2
5Q LOSS WILD-TYPE	172	210	62	163

Figure S307. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.017

Table S308. Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
5Q LOSS MUTATED	15	23	11
5Q LOSS WILD-TYPE	188	167	256

Figure S308. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0015

Table S309. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
5Q LOSS MUTATED	6	17	9	1
5Q LOSS WILD-TYPE	131	90	174	81

Figure S309. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S310. Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
6P LOSS MUTATED	83	31	2
6P LOSS WILD-TYPE	450	511	13

Figure S310. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S311. Gene #52: '6p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
6P LOSS MUTATED	21	11	12	6
6P LOSS WILD-TYPE	163	226	52	159

Figure S311. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S312. Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
6P LOSS MUTATED	41	11	11
6P LOSS WILD-TYPE	192	224	181

Figure S312. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S313. Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
6P LOSS MUTATED	38	12	13
6P LOSS WILD-TYPE	165	178	254

Figure S313. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.01

Table S314. Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
6P LOSS MUTATED	19	3	8
6P LOSS WILD-TYPE	166	158	151

Figure S314. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0044

Table S315. Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
6P LOSS MUTATED	7	4	6	13
6P LOSS WILD-TYPE	84	133	182	76

Figure S315. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S316. Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
6Q LOSS MUTATED	121	66	2
6Q LOSS WILD-TYPE	412	476	13

Figure S316. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00043

Table S317. Gene #53: '6q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
6Q LOSS MUTATED	35	37	14	8
6Q LOSS WILD-TYPE	149	200	50	157

Figure S317. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S318. Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
6Q LOSS MUTATED	57	31	18
6Q LOSS WILD-TYPE	176	204	174

Figure S318. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S319. Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
6Q LOSS MUTATED	52	31	23
6Q LOSS WILD-TYPE	151	159	244

Figure S319. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0023

Table S320. Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
6Q LOSS MUTATED	30	14	16	4
6Q LOSS WILD-TYPE	107	93	167	78

Figure S320. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.044

Table S321. Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
6Q LOSS MUTATED	33	15	14
6Q LOSS WILD-TYPE	152	146	145

Figure S321. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00043

Table S322. Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
6Q LOSS MUTATED	21	8	15	18
6Q LOSS WILD-TYPE	70	129	173	71

Figure S322. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.067

Table S323. Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
7P LOSS MUTATED	0	4	1	2
7P LOSS WILD-TYPE	147	92	151	111

Figure S323. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00035

Table S324. Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
8P LOSS MUTATED	55	19	0
8P LOSS WILD-TYPE	478	523	15

Figure S324. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S325. Gene #56: '8p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
8P LOSS MUTATED	21	6	1	0
8P LOSS WILD-TYPE	163	231	63	165

Figure S325. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S326. Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
8P LOSS MUTATED	25	2	4
8P LOSS WILD-TYPE	208	233	188

Figure S326. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S327. Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
8P LOSS MUTATED	22	6	3
8P LOSS WILD-TYPE	181	184	264

Figure S327. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.075

Table S328. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
8P LOSS MUTATED	8	5	3	0
8P LOSS WILD-TYPE	129	102	180	82

Figure S328. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0034

Table S329. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
8P LOSS MUTATED	6	1	9
8P LOSS WILD-TYPE	216	183	94

Figure S329. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0016

Table S330. Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
8P LOSS MUTATED	1	4	1	9
8P LOSS WILD-TYPE	90	133	187	80

Figure S330. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'MIR_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.077

Table S331. Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
8Q LOSS MUTATED	20	9	6	6
8Q LOSS WILD-TYPE	136	174	81	114

Figure S331. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S332. Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
8Q LOSS MUTATED	45	7	0
8Q LOSS WILD-TYPE	488	535	15

Figure S332. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S333. Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
8Q LOSS MUTATED	17	2	1	0
8Q LOSS WILD-TYPE	167	235	63	165

Figure S333. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S334. Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
8Q LOSS MUTATED	19	1	3
8Q LOSS WILD-TYPE	214	234	189

Figure S334. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S335. Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
8Q LOSS MUTATED	18	3	2
8Q LOSS WILD-TYPE	185	187	265

Figure S335. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.002

Table S336. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
8Q LOSS MUTATED	4	0	7
8Q LOSS WILD-TYPE	218	184	96

Figure S336. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S337. Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
8Q LOSS MUTATED	0	3	0	7
8Q LOSS WILD-TYPE	91	134	188	82

Figure S337. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00347 (Fisher's exact test), Q value = 0.011

Table S338. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
9P LOSS MUTATED	50	19	63	43
9P LOSS WILD-TYPE	97	77	89	70

Figure S338. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S339. Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
9P LOSS MUTATED	190	125	4
9P LOSS WILD-TYPE	343	417	11

Figure S339. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S340. Gene #58: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
9P LOSS MUTATED	68	67	11	23
9P LOSS WILD-TYPE	116	170	53	142

Figure S340. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.019

Table S341. Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
9P LOSS MUTATED	76	49	42
9P LOSS WILD-TYPE	157	186	150

Figure S341. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.029

Table S342. Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
9P LOSS MUTATED	65	49	53
9P LOSS WILD-TYPE	138	141	214

Figure S342. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.073

Table S343. Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
9P LOSS MUTATED	22	23	42	30
9P LOSS WILD-TYPE	69	114	146	59

Figure S343. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.069

Table S344. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
9Q LOSS MUTATED	20	8	21	29
9Q LOSS WILD-TYPE	128	94	79	129

Figure S344. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.058

Table S345. Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
9Q LOSS MUTATED	85	57	1
9Q LOSS WILD-TYPE	448	485	14

Figure S345. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.016

Table S346. Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
9Q LOSS MUTATED	41	20	18
9Q LOSS WILD-TYPE	192	215	174

Figure S346. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.058

Table S347. Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
9Q LOSS MUTATED	35	19	25
9Q LOSS WILD-TYPE	168	171	242

Figure S347. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.049

Table S348. Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
9Q LOSS MUTATED	10	7	18	16
9Q LOSS WILD-TYPE	81	130	170	73

Figure S348. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S349. Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
10P LOSS MUTATED	132	64	140	83
10P LOSS WILD-TYPE	15	32	12	30

Figure S349. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S350. Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
10P LOSS MUTATED	127	62	93	137
10P LOSS WILD-TYPE	21	40	7	21

Figure S350. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.033

Table S351. Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
10P LOSS MUTATED	141	145	67	101
10P LOSS WILD-TYPE	15	38	20	19

Figure S351. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S352. Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
10P LOSS MUTATED	226	108	120
10P LOSS WILD-TYPE	67	16	9

Figure S352. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S353. Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
10P LOSS MUTATED	497	53	13
10P LOSS WILD-TYPE	36	489	2

Figure S353. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S354. Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
10P LOSS MUTATED	171	7	21	7
10P LOSS WILD-TYPE	13	230	43	158

Figure S354. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S355. Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
10P LOSS MUTATED	187	5	22
10P LOSS WILD-TYPE	46	230	170

Figure S355. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S356. Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
10P LOSS MUTATED	181	10	23
10P LOSS WILD-TYPE	22	180	244

Figure S356. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S357. Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
10P LOSS MUTATED	33	26	20	4
10P LOSS WILD-TYPE	104	81	163	78

Figure S357. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S358. Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
10P LOSS MUTATED	11	12	60
10P LOSS WILD-TYPE	211	172	43

Figure S358. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S359. Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
10P LOSS MUTATED	62	3	18
10P LOSS WILD-TYPE	123	158	141

Figure S359. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S360. Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
10P LOSS MUTATED	4	5	11	63
10P LOSS WILD-TYPE	87	132	177	26

Figure S360. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S361. Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
10Q LOSS MUTATED	133	68	145	87
10Q LOSS WILD-TYPE	14	28	7	26

Figure S361. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S362. Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
10Q LOSS MUTATED	128	69	97	139
10Q LOSS WILD-TYPE	20	33	3	19

Figure S362. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CNMF'

P value = 0.00304 (Fisher's exact test), Q value = 0.0096

Table S363. Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
10Q LOSS MUTATED	145	152	67	104
10Q LOSS WILD-TYPE	11	31	20	16

Figure S363. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00071

Table S364. Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
10Q LOSS MUTATED	236	109	123
10Q LOSS WILD-TYPE	57	15	6

Figure S364. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S365. Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
10Q LOSS MUTATED	501	75	15
10Q LOSS WILD-TYPE	32	467	0

Figure S365. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S366. Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
10Q LOSS MUTATED	171	21	21	7
10Q LOSS WILD-TYPE	13	216	43	158

Figure S366. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S367. Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
10Q LOSS MUTATED	193	13	24
10Q LOSS WILD-TYPE	40	222	168

Figure S367. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S368. Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
10Q LOSS MUTATED	184	21	25
10Q LOSS WILD-TYPE	19	169	242

Figure S368. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S369. Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
10Q LOSS MUTATED	36	32	24	5
10Q LOSS WILD-TYPE	101	75	159	77

Figure S369. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S370. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
10Q LOSS MUTATED	15	15	67
10Q LOSS WILD-TYPE	207	169	36

Figure S370. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S371. Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
10Q LOSS MUTATED	68	7	22
10Q LOSS WILD-TYPE	117	154	137

Figure S371. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S372. Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
10Q LOSS MUTATED	7	7	16	67
10Q LOSS WILD-TYPE	84	130	172	22

Figure S372. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S373. Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
11P LOSS MUTATED	27	32	9	22
11P LOSS WILD-TYPE	120	64	143	91

Figure S373. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S374. Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
11P LOSS MUTATED	26	36	4	24
11P LOSS WILD-TYPE	122	66	96	134

Figure S374. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.035

Table S375. Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
11P LOSS MUTATED	63	20	13
11P LOSS WILD-TYPE	230	104	116

Figure S375. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0039

Table S376. Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
11P LOSS MUTATED	80	75	8
11P LOSS WILD-TYPE	453	467	7

Figure S376. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S377. Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
11P LOSS MUTATED	20	52	5	0
11P LOSS WILD-TYPE	164	185	59	165

Figure S377. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0014

Table S378. Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
11P LOSS MUTATED	49	25	16
11P LOSS WILD-TYPE	184	210	176

Figure S378. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S379. Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
11P LOSS MUTATED	33	43	14
11P LOSS WILD-TYPE	170	147	253

Figure S379. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S380. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
11P LOSS MUTATED	14	29	17	4
11P LOSS WILD-TYPE	123	78	166	78

Figure S380. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S381. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11P LOSS MUTATED	23	14	27
11P LOSS WILD-TYPE	199	170	76

Figure S381. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.042

Table S382. Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11P LOSS MUTATED	11	16	16	20
11P LOSS WILD-TYPE	80	121	172	69

Figure S382. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S383. Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
11Q LOSS MUTATED	31	28	10	16
11Q LOSS WILD-TYPE	116	68	142	97

Figure S383. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00082

Table S384. Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
11Q LOSS MUTATED	28	27	5	25
11Q LOSS WILD-TYPE	120	75	95	133

Figure S384. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S385. Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
11Q LOSS MUTATED	84	22	7
11Q LOSS WILD-TYPE	449	520	8

Figure S385. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00026

Table S386. Gene #63: '11q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
11Q LOSS MUTATED	18	11	4	0
11Q LOSS WILD-TYPE	166	226	60	165

Figure S386. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S387. Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
11Q LOSS MUTATED	39	3	4
11Q LOSS WILD-TYPE	194	232	188

Figure S387. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S388. Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
11Q LOSS MUTATED	32	10	4
11Q LOSS WILD-TYPE	171	180	263

Figure S388. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.059

Table S389. Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
11Q LOSS MUTATED	7	9	6	0
11Q LOSS WILD-TYPE	130	98	177	82

Figure S389. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00082

Table S390. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
11Q LOSS MUTATED	6	3	13
11Q LOSS WILD-TYPE	216	181	90

Figure S390. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0036

Table S391. Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
11Q LOSS MUTATED	2	5	3	11
11Q LOSS WILD-TYPE	89	132	185	78

Figure S391. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.061

Table S392. Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
12P LOSS MUTATED	45	37	4
12P LOSS WILD-TYPE	488	505	11

Figure S392. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.097

Table S393. Gene #64: '12p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
12P LOSS MUTATED	8	22	3	5
12P LOSS WILD-TYPE	176	215	61	160

Figure S393. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.044

Table S394. Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
12P LOSS MUTATED	15	18	9
12P LOSS WILD-TYPE	188	172	258

Figure S394. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.016

Table S395. Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
12Q LOSS MUTATED	43	61	5
12Q LOSS WILD-TYPE	490	481	10

Figure S395. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S396. Gene #65: '12q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
12Q LOSS MUTATED	7	46	5	5
12Q LOSS WILD-TYPE	177	191	59	160

Figure S396. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S397. Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
12Q LOSS MUTATED	15	36	16
12Q LOSS WILD-TYPE	188	154	251

Figure S397. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.025

Table S398. Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
12Q LOSS MUTATED	9	21	17	6
12Q LOSS WILD-TYPE	128	86	166	76

Figure S398. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S399. Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
13Q LOSS MUTATED	57	35	26	45
13Q LOSS WILD-TYPE	90	61	126	68

Figure S399. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0058

Table S400. Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
13Q LOSS MUTATED	50	41	17	55
13Q LOSS WILD-TYPE	98	61	83	103

Figure S400. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S401. Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
13Q LOSS MUTATED	168	121	9
13Q LOSS WILD-TYPE	365	421	6

Figure S401. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.042

Table S402. Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
13Q LOSS MUTATED	53	59	11	26
13Q LOSS WILD-TYPE	131	178	53	139

Figure S402. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0018

Table S403. Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
13Q LOSS MUTATED	74	54	30
13Q LOSS WILD-TYPE	159	181	162

Figure S403. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0016

Table S404. Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
13Q LOSS MUTATED	59	56	43
13Q LOSS WILD-TYPE	144	134	224

Figure S404. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00929 (Fisher's exact test), Q value = 0.025

Table S405. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
13Q LOSS MUTATED	52	28	31
13Q LOSS WILD-TYPE	170	156	72

Figure S405. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S406. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
14Q LOSS MUTATED	46	33	17	39
14Q LOSS WILD-TYPE	101	63	135	74

Figure S406. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00048

Table S407. Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
14Q LOSS MUTATED	43	35	10	47
14Q LOSS WILD-TYPE	105	67	90	111

Figure S407. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S408. Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
14Q LOSS MUTATED	137	80	8
14Q LOSS WILD-TYPE	396	462	7

Figure S408. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00052

Table S409. Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
14Q LOSS MUTATED	51	30	15	20
14Q LOSS WILD-TYPE	133	207	49	145

Figure S409. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S410. Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
14Q LOSS MUTATED	75	26	28
14Q LOSS WILD-TYPE	158	209	164

Figure S410. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S411. Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
14Q LOSS MUTATED	66	29	34
14Q LOSS WILD-TYPE	137	161	233

Figure S411. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.0099

Table S412. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
14Q LOSS MUTATED	35	12	22	9
14Q LOSS WILD-TYPE	102	95	161	73

Figure S412. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.0061

Table S413. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
14Q LOSS MUTATED	28	22	28
14Q LOSS WILD-TYPE	194	162	75

Figure S413. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00857 (Fisher's exact test), Q value = 0.023

Table S414. Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
14Q LOSS MUTATED	41	18	19
14Q LOSS WILD-TYPE	144	143	140

Figure S414. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0027

Table S415. Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
14Q LOSS MUTATED	14	15	22	27
14Q LOSS WILD-TYPE	77	122	166	62

Figure S415. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00031

Table S416. Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
15Q LOSS MUTATED	26	26	12	31
15Q LOSS WILD-TYPE	121	70	140	82

Figure S416. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S417. Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
15Q LOSS MUTATED	22	37	7	29
15Q LOSS WILD-TYPE	126	65	93	129

Figure S417. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.012

Table S418. Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
15Q LOSS MUTATED	21	48	15	14
15Q LOSS WILD-TYPE	135	135	72	106

Figure S418. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00352 (Fisher's exact test), Q value = 0.011

Table S419. Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
15Q LOSS MUTATED	65	11	22
15Q LOSS WILD-TYPE	228	113	107

Figure S419. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.091

Table S420. Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
15Q LOSS MUTATED	89	64	3
15Q LOSS WILD-TYPE	444	478	12

Figure S420. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0049

Table S421. Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
15Q LOSS MUTATED	23	19	1	28
15Q LOSS WILD-TYPE	161	218	63	137

Figure S421. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S422. Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
16P LOSS MUTATED	56	19	3
16P LOSS WILD-TYPE	477	523	12

Figure S422. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.011

Table S423. Gene #69: '16p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
16P LOSS MUTATED	17	9	2	2
16P LOSS WILD-TYPE	167	228	62	163

Figure S423. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S424. Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
16P LOSS MUTATED	26	6	6
16P LOSS WILD-TYPE	207	229	186

Figure S424. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0015

Table S425. Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
16P LOSS MUTATED	23	5	10
16P LOSS WILD-TYPE	180	185	257

Figure S425. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S426. Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
16Q LOSS MUTATED	77	24	4
16Q LOSS WILD-TYPE	456	518	11

Figure S426. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S427. Gene #70: '16q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
16Q LOSS MUTATED	29	11	3	3
16Q LOSS WILD-TYPE	155	226	61	162

Figure S427. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S428. Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
16Q LOSS MUTATED	35	8	7
16Q LOSS WILD-TYPE	198	227	185

Figure S428. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S429. Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
16Q LOSS MUTATED	32	7	11
16Q LOSS WILD-TYPE	171	183	256

Figure S429. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.011

Table S430. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
16Q LOSS MUTATED	7	4	11
16Q LOSS WILD-TYPE	215	180	92

Figure S430. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00867 (Fisher's exact test), Q value = 0.024

Table S431. Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
16Q LOSS MUTATED	3	4	4	10
16Q LOSS WILD-TYPE	88	133	184	79

Figure S431. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.056

Table S432. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
17P LOSS MUTATED	25	12	10	9
17P LOSS WILD-TYPE	122	84	142	104

Figure S432. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.06

Table S433. Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
17P LOSS MUTATED	23	15	8	10
17P LOSS WILD-TYPE	125	87	92	148

Figure S433. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S434. Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
17P LOSS MUTATED	54	19	4
17P LOSS WILD-TYPE	479	523	11

Figure S434. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0021

Table S435. Gene #71: '17p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
17P LOSS MUTATED	18	6	3	2
17P LOSS WILD-TYPE	166	231	61	163

Figure S435. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S436. Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
17P LOSS MUTATED	27	4	3
17P LOSS WILD-TYPE	206	231	189

Figure S436. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S437. Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
17P LOSS MUTATED	23	7	4
17P LOSS WILD-TYPE	180	183	263

Figure S437. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00666 (Fisher's exact test), Q value = 0.019

Table S438. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
17P LOSS MUTATED	5	1	7
17P LOSS WILD-TYPE	217	183	96

Figure S438. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.031

Table S439. Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
17P LOSS MUTATED	3	2	1	6
17P LOSS WILD-TYPE	88	135	187	83

Figure S439. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.014

Table S440. Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
17Q LOSS MUTATED	19	7	9	2
17Q LOSS WILD-TYPE	128	89	143	111

Figure S440. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.087

Table S441. Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
17Q LOSS MUTATED	15	15	11
17Q LOSS WILD-TYPE	278	109	118

Figure S441. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00086

Table S442. Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
17Q LOSS MUTATED	37	12	2
17Q LOSS WILD-TYPE	496	530	13

Figure S442. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0091

Table S443. Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
17Q LOSS MUTATED	12	3	2	1
17Q LOSS WILD-TYPE	172	234	62	164

Figure S443. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0047

Table S444. Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
17Q LOSS MUTATED	15	3	2
17Q LOSS WILD-TYPE	218	232	190

Figure S444. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0019

Table S445. Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
17Q LOSS MUTATED	14	4	2
17Q LOSS WILD-TYPE	189	186	265

Figure S445. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.053

Table S446. Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
17Q LOSS MUTATED	3	0	1	3
17Q LOSS WILD-TYPE	88	137	187	86

Figure S446. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.094

Table S447. Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
18P LOSS MUTATED	20	15	9	15
18P LOSS WILD-TYPE	127	81	143	98

Figure S447. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.069

Table S448. Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
18P LOSS MUTATED	19	16	4	20
18P LOSS WILD-TYPE	129	86	96	138

Figure S448. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.059

Table S449. Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
18P LOSS MUTATED	29	22	6	31
18P LOSS WILD-TYPE	155	215	58	134

Figure S449. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00856 (Fisher's exact test), Q value = 0.023

Table S450. Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
18Q LOSS MUTATED	18	12	2	20
18Q LOSS WILD-TYPE	130	90	98	138

Figure S450. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0036

Table S451. Gene #74: '18q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
18Q LOSS MUTATED	19	19	4	34
18Q LOSS WILD-TYPE	165	218	60	131

Figure S451. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0032

Table S452. Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
19P LOSS MUTATED	3	10	2	9
19P LOSS WILD-TYPE	144	86	150	104

Figure S452. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.0093

Table S453. Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
19P LOSS MUTATED	4	12	1	7
19P LOSS WILD-TYPE	144	90	99	151

Figure S453. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00961 (Fisher's exact test), Q value = 0.026

Table S454. Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
19P LOSS MUTATED	17	39	1
19P LOSS WILD-TYPE	516	503	14

Figure S454. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.016

Table S455. Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
19P LOSS MUTATED	6	18	6
19P LOSS WILD-TYPE	179	143	153

Figure S455. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MRNA_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.019

Table S456. Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
19Q LOSS MUTATED	6	10	3	11
19Q LOSS WILD-TYPE	141	86	149	102

Figure S456. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.03

Table S457. Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
19Q LOSS MUTATED	7	12	1	10
19Q LOSS WILD-TYPE	141	90	99	148

Figure S457. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S458. Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
19Q LOSS MUTATED	23	220	1
19Q LOSS WILD-TYPE	510	322	14

Figure S458. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S459. Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
19Q LOSS MUTATED	11	31	12	164
19Q LOSS WILD-TYPE	173	206	52	1

Figure S459. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S460. Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
19Q LOSS MUTATED	19	98	104
19Q LOSS WILD-TYPE	214	137	88

Figure S460. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S461. Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
19Q LOSS MUTATED	12	30	179
19Q LOSS WILD-TYPE	191	160	88

Figure S461. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S462. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
19Q LOSS MUTATED	31	23	88	68
19Q LOSS WILD-TYPE	106	84	95	14

Figure S462. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S463. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
19Q LOSS MUTATED	97	103	10
19Q LOSS WILD-TYPE	125	81	93

Figure S463. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S464. Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
19Q LOSS MUTATED	34	96	79
19Q LOSS WILD-TYPE	151	65	80

Figure S464. Get High-res Image Gene #76: '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 = 6.1e-05

Table S465. Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
19Q LOSS MUTATED	11	92	97	9
19Q LOSS WILD-TYPE	80	45	91	80

Figure S465. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00071

Table S466. Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
20P LOSS MUTATED	4	10	0	3
20P LOSS WILD-TYPE	143	86	152	110

Figure S466. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S467. Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
20P LOSS MUTATED	5	11	0	1
20P LOSS WILD-TYPE	143	91	100	157

Figure S467. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'MIR_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.076

Table S468. Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
20P LOSS MUTATED	2	7	7	2
20P LOSS WILD-TYPE	154	176	80	118

Figure S468. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'20q loss' versus 'MRNA_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0049

Table S469. Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
20Q LOSS MUTATED	4	8	0	3
20Q LOSS WILD-TYPE	143	88	152	110

Figure S469. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S470. Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
20Q LOSS MUTATED	4	10	0	1
20Q LOSS WILD-TYPE	144	92	100	157

Figure S470. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00545 (Fisher's exact test), Q value = 0.016

Table S471. Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
20Q LOSS MUTATED	14	5	2
20Q LOSS WILD-TYPE	519	537	13

Figure S471. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.032

Table S472. Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
20Q LOSS MUTATED	2	5	0
20Q LOSS WILD-TYPE	201	185	267

Figure S472. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.052

Table S473. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
21Q LOSS MUTATED	4	12	10	10
21Q LOSS WILD-TYPE	143	84	142	103

Figure S473. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0046

Table S474. Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
21Q LOSS MUTATED	5	17	6	8
21Q LOSS WILD-TYPE	143	85	94	150

Figure S474. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S475. Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
21Q LOSS MUTATED	9	31	4	2
21Q LOSS WILD-TYPE	175	206	60	163

Figure S475. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S476. Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
21Q LOSS MUTATED	10	28	8
21Q LOSS WILD-TYPE	193	162	259

Figure S476. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S477. Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
22Q LOSS MUTATED	177	58	5
22Q LOSS WILD-TYPE	356	484	10

Figure S477. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S478. Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
22Q LOSS MUTATED	58	27	13	5
22Q LOSS WILD-TYPE	126	210	51	160

Figure S478. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S479. Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
22Q LOSS MUTATED	73	20	18
22Q LOSS WILD-TYPE	160	215	174

Figure S479. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S480. Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
22Q LOSS MUTATED	69	23	19
22Q LOSS WILD-TYPE	134	167	248

Figure S480. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S481. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
22Q LOSS MUTATED	18	15	24
22Q LOSS WILD-TYPE	204	169	79

Figure S481. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.031

Table S482. Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
22Q LOSS MUTATED	31	13	12
22Q LOSS WILD-TYPE	154	148	147

Figure S482. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S483. Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
22Q LOSS MUTATED	5	13	15	23
22Q LOSS WILD-TYPE	86	124	173	66

Figure S483. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.018

Table S484. Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
XP LOSS MUTATED	20	31	28	22
XP LOSS WILD-TYPE	127	65	124	91

Figure S484. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00795 (Fisher's exact test), Q value = 0.022

Table S485. Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
XP LOSS MUTATED	20	32	19	30
XP LOSS WILD-TYPE	128	70	81	128

Figure S485. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'MIR_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.066

Table S486. Gene #81: 'xp loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
XP LOSS MUTATED	24	48	17	17
XP LOSS WILD-TYPE	132	135	70	103

Figure S486. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'MIR_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00935 (Fisher's exact test), Q value = 0.025

Table S487. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
XP LOSS MUTATED	60	52	27
XP LOSS WILD-TYPE	173	183	165

Figure S487. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.034

Table S488. Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
XP LOSS MUTATED	44	52	43
XP LOSS WILD-TYPE	159	138	224

Figure S488. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.079

Table S489. Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
XP LOSS MUTATED	23	25	28	24
XP LOSS WILD-TYPE	114	82	155	58

Figure S489. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.08

Table S490. Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
XP LOSS MUTATED	40	38	21
XP LOSS WILD-TYPE	145	123	138

Figure S490. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.042

Table S491. Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
XQ LOSS MUTATED	19	28	26	19
XQ LOSS WILD-TYPE	128	68	126	94

Figure S491. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.058

Table S492. Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
XQ LOSS MUTATED	18	28	18	28
XQ LOSS WILD-TYPE	130	74	82	130

Figure S492. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.0088

Table S493. Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
XQ LOSS MUTATED	39	30	3	32
XQ LOSS WILD-TYPE	145	207	61	133

Figure S493. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0036

Table S494. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
XQ LOSS MUTATED	53	33	19
XQ LOSS WILD-TYPE	180	202	173

Figure S494. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00043

Table S495. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
XQ LOSS MUTATED	12	17	17	24
XQ LOSS WILD-TYPE	125	90	166	58

Figure S495. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.066

Table S496. Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
XQ LOSS MUTATED	10	27	17	15
XQ LOSS WILD-TYPE	81	110	171	74

Figure S496. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBMLGG-TP/15101903/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBMLGG-TP/15249296/GBMLGG-TP.transferedmergedcluster.txt
Number of patients = 1090
Number of significantly arm-level cnvs = 82
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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