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

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X065WF

Overview

Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 524 patients, 377 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 377 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
8p loss	75 (14%)	449	0.00791 (1.00)	0.00011 (0.0595)	1e-05 (0.00892)	1e-05 (0.00892)	0.034 (1.00)	0.0255 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	5e-05 (0.028)
9q loss	117 (22%)	407	3e-05 (0.017)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0003 (0.156)	0.7 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00185 (0.866)	0.00462 (1.00)
15q loss	106 (20%)	418	0.00062 (0.316)	2e-05 (0.0118)	1e-05 (0.00892)	1e-05 (0.00892)	0.00082 (0.407)	0.487 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)
5p gain	49 (9%)	475	0.901 (1.00)	0.219 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0592 (1.00)	0.428 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	0.00016 (0.0856)
18p gain	68 (13%)	456	0.334 (1.00)	0.241 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0127 (1.00)	0.163 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)
4p loss	100 (19%)	424	0.00372 (1.00)	0.00137 (0.651)	1e-05 (0.00892)	1e-05 (0.00892)	0.00109 (0.529)	0.186 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	3e-05 (0.017)	2e-05 (0.0118)
4q loss	99 (19%)	425	0.152 (1.00)	0.00524 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0138 (1.00)	0.188 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)
11q loss	68 (13%)	456			1e-05 (0.00892)	1e-05 (0.00892)	0.851 (1.00)	0.79 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0003 (0.156)	0.00044 (0.227)
16p loss	94 (18%)	430	0.00182 (0.854)	0.0077 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0934 (1.00)	0.318 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0001 (0.0542)	0.00028 (0.147)
16q loss	135 (26%)	389	0.00086 (0.426)	0.00156 (0.735)	1e-05 (0.00892)	1e-05 (0.00892)	0.343 (1.00)	0.973 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	6e-05 (0.0332)
19p loss	57 (11%)	467			1e-05 (0.00892)	1e-05 (0.00892)	0.0817 (1.00)	0.216 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	3e-05 (0.017)	0.00015 (0.0804)
21q loss	53 (10%)	471	0.00765 (1.00)	0.00497 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.128 (1.00)	0.328 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00028 (0.147)
xq loss	69 (13%)	455	0.00785 (1.00)	0.00498 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00017 (0.0904)	0.214 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00071 (0.356)	2e-05 (0.0118)
2p gain	92 (18%)	432	0.855 (1.00)	0.37 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0574 (1.00)	0.24 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00021 (0.111)	0.00107 (0.52)
2q gain	75 (14%)	449	0.341 (1.00)	0.601 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0634 (1.00)	0.134 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00027 (0.142)	0.00262 (1.00)
18q gain	41 (8%)	483	0.253 (1.00)	0.0448 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.278 (1.00)	0.095 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	5e-05 (0.028)	0.00466 (1.00)
20p gain	107 (20%)	417	0.00818 (1.00)	0.0499 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.163 (1.00)	0.741 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	8e-05 (0.0438)	0.00105 (0.511)
20q gain	125 (24%)	399	0.00212 (0.982)	0.00723 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0325 (1.00)	0.67 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00021 (0.111)	0.00336 (1.00)
22q gain	31 (6%)	493			1e-05 (0.00892)	1e-05 (0.00892)	0.372 (1.00)	0.186 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0161 (1.00)
5q loss	72 (14%)	452	0.013 (1.00)	0.00974 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00129 (0.618)	0.00223 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	0.00068 (0.343)
9p loss	99 (19%)	425	0.001 (0.488)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00406 (1.00)	0.565 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00571 (1.00)	0.033 (1.00)
14q loss	56 (11%)	468	0.00185 (0.866)	0.00056 (0.287)	1e-05 (0.00892)	1e-05 (0.00892)	0.0253 (1.00)	0.075 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	0.00123 (0.59)
17p loss	122 (23%)	402	0.0035 (1.00)	0.00016 (0.0856)	1e-05 (0.00892)	1e-05 (0.00892)	0.00372 (1.00)	0.371 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00065 (0.328)	0.00746 (1.00)
17q loss	88 (17%)	436	0.00215 (0.993)	2e-05 (0.0118)	1e-05 (0.00892)	1e-05 (0.00892)	0.109 (1.00)	0.919 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0123 (1.00)	0.00524 (1.00)
3q gain	78 (15%)	446	0.618 (1.00)	0.25 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.105 (1.00)	0.161 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0005 (0.257)	0.00228 (1.00)
6p gain	76 (15%)	448	0.212 (1.00)	0.663 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0994 (1.00)	0.834 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0186 (1.00)	0.0629 (1.00)
13q gain	28 (5%)	496	0.137 (1.00)	0.00635 (1.00)	1e-05 (0.00892)	0.00016 (0.0856)	0.252 (1.00)	0.0113 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0405 (1.00)	0.0847 (1.00)
19p gain	50 (10%)	474	0.0412 (1.00)	0.0302 (1.00)	1e-05 (0.00892)	0.00024 (0.126)	0.908 (1.00)	0.0731 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	0.0623 (1.00)	0.354 (1.00)
19q gain	55 (10%)	469			1e-05 (0.00892)	1e-05 (0.00892)	0.487 (1.00)	0.0439 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00745 (1.00)	0.0802 (1.00)
1p loss	22 (4%)	502			1e-05 (0.00892)	1e-05 (0.00892)	0.787 (1.00)	0.362 (1.00)	5e-05 (0.028)	1e-05 (0.00892)	7e-05 (0.0384)	6e-05 (0.0332)	0.0262 (1.00)	0.0308 (1.00)
1q loss	13 (2%)	511			9e-05 (0.049)	2e-05 (0.0118)			3e-05 (0.017)	7e-05 (0.0384)	5e-05 (0.028)	0.00011 (0.0595)	0.0443 (1.00)	0.0708 (1.00)
3p loss	50 (10%)	474	0.0386 (1.00)	0.0007 (0.351)	1e-05 (0.00892)	1e-05 (0.00892)	0.0217 (1.00)	0.125 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00472 (1.00)	0.00315 (1.00)
3q loss	30 (6%)	494	0.0396 (1.00)	0.00064 (0.324)	1e-05 (0.00892)	0.00011 (0.0595)	0.0656 (1.00)	0.264 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.114 (1.00)	0.236 (1.00)
5p loss	54 (10%)	470	0.15 (1.00)	0.114 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.00662 (1.00)	0.216 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00262 (1.00)	0.00719 (1.00)
7q loss	41 (8%)	483			1e-05 (0.00892)	1e-05 (0.00892)	0.0469 (1.00)	0.015 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00344 (1.00)	0.00752 (1.00)
8q loss	25 (5%)	499			1e-05 (0.00892)	1e-05 (0.00892)	0.329 (1.00)	0.838 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00202 (0.939)	0.00729 (1.00)
10p loss	40 (8%)	484	0.039 (1.00)	0.0303 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0565 (1.00)	0.185 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00541 (1.00)	0.0274 (1.00)
10q loss	39 (7%)	485	0.137 (1.00)	0.166 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0541 (1.00)	0.169 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	2e-05 (0.0118)	0.0334 (1.00)	0.0568 (1.00)
11p loss	72 (14%)	452			1e-05 (0.00892)	1e-05 (0.00892)	0.299 (1.00)	0.333 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00057 (0.291)	0.00206 (0.956)
12p loss	42 (8%)	482	0.136 (1.00)	0.167 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0418 (1.00)	0.0381 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00136 (0.647)	0.00719 (1.00)
12q loss	34 (6%)	490			1e-05 (0.00892)	1e-05 (0.00892)	0.102 (1.00)	0.0155 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	6e-05 (0.0332)	1e-05 (0.00892)	0.00069 (0.347)	0.00452 (1.00)
13q loss	89 (17%)	435	0.903 (1.00)	0.194 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0247 (1.00)	0.499 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0483 (1.00)	0.0453 (1.00)
18q loss	65 (12%)	459	0.537 (1.00)	0.513 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.53 (1.00)	1 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.00315 (1.00)	0.00513 (1.00)
19q loss	53 (10%)	471	0.254 (1.00)	0.0179 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.196 (1.00)	0.696 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	2e-05 (0.0118)	0.00088 (0.434)	0.00875 (1.00)
22q loss	105 (20%)	419	0.00226 (1.00)	0.00718 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	0.0402 (1.00)	0.28 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.0208 (1.00)	0.0442 (1.00)
1p gain	46 (9%)	478	0.535 (1.00)	0.218 (1.00)	1e-05 (0.00892)	0.0012 (0.578)	0.0447 (1.00)	0.263 (1.00)	2e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.00892)	1e-05 (0.00892)	0.00151 (0.714)	0.00749 (1.00)
17q gain	28 (5%)	496			1e-05 (0.00892)	2e-05 (0.0118)	0.0415 (1.00)	1 (1.00)	0.00014 (0.0752)	1e-05 (0.00892)	8e-05 (0.0438)	0.00089 (0.436)	0.0626 (1.00)	0.213 (1.00)
21q gain	36 (7%)	488			1e-05 (0.00892)	0.00137 (0.651)	0.375 (1.00)	0.838 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.221 (1.00)	0.244 (1.00)
6q loss	24 (5%)	500	0.38 (1.00)	0.0299 (1.00)	1e-05 (0.00892)	5e-05 (0.028)	0.48 (1.00)	0.802 (1.00)	2e-05 (0.0118)	1e-05 (0.00892)	0.00406 (1.00)	3e-05 (0.017)	0.111 (1.00)	0.0495 (1.00)
7p loss	43 (8%)	481	0.0393 (1.00)	0.194 (1.00)	1e-05 (0.00892)	0.00062 (0.316)	0.0384 (1.00)	0.55 (1.00)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	1e-05 (0.00892)	0.128 (1.00)	0.526 (1.00)
18p loss	52 (10%)	472			1e-05 (0.00892)	1e-05 (0.00892)	0.474 (1.00)	0.567 (1.00)	1e-05 (0.00892)	0.00531 (1.00)	0.00013 (0.0699)	0.00029 (0.151)	0.00491 (1.00)	0.00834 (1.00)
12p gain	66 (13%)	458	0.385 (1.00)	0.689 (1.00)	1e-05 (0.00892)	3e-05 (0.017)	0.915 (1.00)	0.97 (1.00)	2e-05 (0.0118)	8e-05 (0.0438)	0.00073 (0.364)	0.00059 (0.301)	0.00154 (0.727)	0.0475 (1.00)
14q gain	36 (7%)	488	1 (1.00)	0.843 (1.00)	1e-05 (0.00892)	0.00097 (0.474)	0.0855 (1.00)	0.693 (1.00)	1e-05 (0.00892)	6e-05 (0.0332)	0.00119 (0.576)	9e-05 (0.049)	0.308 (1.00)	0.624 (1.00)
1q gain	178 (34%)	346	0.179 (1.00)	0.0102 (1.00)	0.00019 (0.101)	0.18 (1.00)	0.0925 (1.00)	0.0154 (1.00)	0.00023 (0.121)	0.00383 (1.00)	1e-05 (0.00892)	0.0464 (1.00)	0.961 (1.00)	0.271 (1.00)
6q gain	61 (12%)	463	0.209 (1.00)	0.662 (1.00)	1e-05 (0.00892)	0.00078 (0.388)	0.0523 (1.00)	0.757 (1.00)	1e-05 (0.00892)	0.0013 (0.621)	0.00087 (0.43)	0.00034 (0.176)	0.41 (1.00)	0.485 (1.00)
8q gain	152 (29%)	372	0.0109 (1.00)	0.03 (1.00)	1e-05 (0.00892)	0.145 (1.00)	0.00018 (0.0956)	0.0222 (1.00)	2e-05 (0.0118)	0.00188 (0.876)	0.00088 (0.434)	0.00445 (1.00)	0.135 (1.00)	0.335 (1.00)
3p gain	45 (9%)	479			1e-05 (0.00892)	0.0177 (1.00)	0.301 (1.00)	0.946 (1.00)	6e-05 (0.0332)	0.0204 (1.00)	0.0039 (1.00)	0.00769 (1.00)	0.0443 (1.00)	0.189 (1.00)
5q gain	19 (4%)	505			1e-05 (0.00892)	0.0599 (1.00)	0.368 (1.00)	0.292 (1.00)	0.00028 (0.147)	0.00122 (0.587)	0.0024 (1.00)	0.00609 (1.00)	0.0323 (1.00)	0.00343 (1.00)
6p loss	17 (3%)	507	0.38 (1.00)	0.03 (1.00)	1e-05 (0.00892)	0.00223 (1.00)	0.363 (1.00)	1 (1.00)	0.00062 (0.316)	1e-05 (0.00892)	0.0639 (1.00)	0.00356 (1.00)	0.189 (1.00)	0.204 (1.00)
4p gain	13 (2%)	511			5e-05 (0.028)	0.913 (1.00)	0.372 (1.00)	0.0371 (1.00)	0.0013 (0.621)	0.0197 (1.00)	0.00723 (1.00)	0.0114 (1.00)	0.164 (1.00)	0.436 (1.00)
7p gain	64 (12%)	460	0.855 (1.00)	0.905 (1.00)	1e-05 (0.00892)	0.00072 (0.359)	0.847 (1.00)	0.864 (1.00)	0.0242 (1.00)	0.0967 (1.00)	0.0199 (1.00)	0.386 (1.00)	0.269 (1.00)	0.411 (1.00)
7q gain	62 (12%)	462	0.854 (1.00)	0.906 (1.00)	1e-05 (0.00892)	0.00056 (0.287)	0.854 (1.00)	0.531 (1.00)	0.157 (1.00)	0.205 (1.00)	0.14 (1.00)	0.586 (1.00)	0.741 (1.00)	0.98 (1.00)
8p gain	116 (22%)	408	0.355 (1.00)	0.407 (1.00)	1e-05 (0.00892)	0.921 (1.00)	0.0208 (1.00)	0.216 (1.00)	0.164 (1.00)	0.66 (1.00)	0.204 (1.00)	0.113 (1.00)	0.61 (1.00)	0.314 (1.00)
10p gain	116 (22%)	408	0.00746 (1.00)	0.0891 (1.00)	1e-05 (0.00892)	0.839 (1.00)	0.194 (1.00)	0.816 (1.00)	0.101 (1.00)	0.21 (1.00)	0.619 (1.00)	0.0077 (1.00)	0.173 (1.00)	0.0475 (1.00)
10q gain	109 (21%)	415	0.00505 (1.00)	0.0889 (1.00)	1e-05 (0.00892)	0.757 (1.00)	0.121 (1.00)	0.659 (1.00)	0.177 (1.00)	0.326 (1.00)	0.441 (1.00)	0.00283 (1.00)	0.18 (1.00)	0.0887 (1.00)
11p gain	22 (4%)	502	0.0382 (1.00)	0.195 (1.00)	1e-05 (0.00892)	0.0765 (1.00)	0.0553 (1.00)	0.113 (1.00)	0.0042 (1.00)	0.00734 (1.00)	0.00476 (1.00)	0.0532 (1.00)	0.209 (1.00)	0.802 (1.00)
11q gain	19 (4%)	505			1e-05 (0.00892)	0.113 (1.00)	0.181 (1.00)	0.0119 (1.00)	0.0285 (1.00)	0.137 (1.00)	0.0732 (1.00)	0.326 (1.00)	0.689 (1.00)	0.94 (1.00)
12q gain	52 (10%)	472	0.387 (1.00)	0.69 (1.00)	1e-05 (0.00892)	0.00443 (1.00)	0.962 (1.00)	0.981 (1.00)	0.0016 (0.752)	0.00893 (1.00)	0.0311 (1.00)	0.0716 (1.00)	0.0664 (1.00)	0.446 (1.00)
16p gain	25 (5%)	499			1e-05 (0.00892)	0.00629 (1.00)	0.178 (1.00)	0.632 (1.00)	0.117 (1.00)	0.179 (1.00)	0.0123 (1.00)	0.0479 (1.00)	0.731 (1.00)	0.877 (1.00)
17p gain	12 (2%)	512			0.00043 (0.222)	0.16 (1.00)	0.225 (1.00)	1 (1.00)	0.0976 (1.00)	0.00309 (1.00)	0.0829 (1.00)	0.0847 (1.00)	0.713 (1.00)	0.303 (1.00)
xq gain	63 (12%)	461	0.703 (1.00)	0.928 (1.00)	1e-05 (0.00892)	0.502 (1.00)	0.871 (1.00)	0.337 (1.00)	0.549 (1.00)	0.342 (1.00)	0.528 (1.00)	0.876 (1.00)	0.171 (1.00)	0.517 (1.00)
2q loss	16 (3%)	508			1e-05 (0.00892)	0.155 (1.00)			0.00071 (0.356)	0.105 (1.00)	0.0376 (1.00)	0.0758 (1.00)	0.829 (1.00)	0.576 (1.00)
20p loss	18 (3%)	506			5e-05 (0.028)	0.323 (1.00)	0.466 (1.00)	0.665 (1.00)	0.0272 (1.00)	0.00384 (1.00)	0.0687 (1.00)	0.0921 (1.00)	0.519 (1.00)	0.659 (1.00)
4q gain	8 (2%)	516			0.00386 (1.00)	0.619 (1.00)			0.0308 (1.00)	0.145 (1.00)	0.27 (1.00)	0.126 (1.00)	0.549 (1.00)	0.423 (1.00)
9p gain	22 (4%)	502			0.00051 (0.262)	0.00279 (1.00)	0.095 (1.00)	0.325 (1.00)	0.00446 (1.00)	0.0682 (1.00)	0.00409 (1.00)	0.0244 (1.00)	0.352 (1.00)	0.533 (1.00)
9q gain	9 (2%)	515			0.0991 (1.00)	0.149 (1.00)			0.364 (1.00)	0.697 (1.00)	0.173 (1.00)	0.684 (1.00)	0.335 (1.00)	0.547 (1.00)
15q gain	11 (2%)	513			0.00519 (1.00)	0.915 (1.00)			0.691 (1.00)	0.506 (1.00)	0.465 (1.00)	0.792 (1.00)	0.57 (1.00)	0.579 (1.00)
16q gain	9 (2%)	515			0.0217 (1.00)	0.0916 (1.00)	0.947 (1.00)	0.842 (1.00)	0.171 (1.00)	0.27 (1.00)	0.173 (1.00)	0.445 (1.00)	0.767 (1.00)	0.127 (1.00)
2p loss	10 (2%)	514			0.00088 (0.434)	0.38 (1.00)			0.00733 (1.00)	0.143 (1.00)	0.614 (1.00)	0.684 (1.00)	0.91 (1.00)	1 (1.00)
20q loss	9 (2%)	515			0.00119 (0.576)	0.0882 (1.00)	0.642 (1.00)	1 (1.00)	0.0369 (1.00)	0.00294 (1.00)	0.297 (1.00)	0.116 (1.00)	0.281 (1.00)	0.181 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1P GAIN MUTATED	6	5	34	1	0
1P GAIN WILD-TYPE	299	43	120	11	5

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S2. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1P GAIN MUTATED	36	5	5
1P GAIN WILD-TYPE	188	145	140

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S3. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
1P GAIN MUTATED	29	11	6
1P GAIN WILD-TYPE	134	202	137

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S4. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
1P GAIN MUTATED	10	33	2
1P GAIN WILD-TYPE	131	186	153

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S5. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
1P GAIN MUTATED	1	29	2	13
1P GAIN WILD-TYPE	54	133	114	169

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S6. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1Q GAIN MUTATED	91	26	50	6	5
1Q GAIN WILD-TYPE	214	22	104	6	0

Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S7. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1Q GAIN MUTATED	70	70	36
1Q GAIN WILD-TYPE	154	80	109

Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S8. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
1Q GAIN MUTATED	72	66	39
1Q GAIN WILD-TYPE	69	153	116

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
2P GAIN MUTATED	9	24	56	2	1
2P GAIN WILD-TYPE	296	24	98	10	4

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S10. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
2P GAIN MUTATED	50	9	11
2P GAIN WILD-TYPE	108	77	155

Figure S10. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S11. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
2P GAIN MUTATED	66	16	9
2P GAIN WILD-TYPE	158	134	136

Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S12. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
2P GAIN MUTATED	57	25	9
2P GAIN WILD-TYPE	106	188	134

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S13. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
2P GAIN MUTATED	16	64	11
2P GAIN WILD-TYPE	125	155	144

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S14. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
2P GAIN MUTATED	8	54	9	20
2P GAIN WILD-TYPE	47	108	107	162

Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S15. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
2P GAIN MUTATED	8	42	18
2P GAIN WILD-TYPE	113	135	76

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S16. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
2Q GAIN MUTATED	6	22	45	1	1
2Q GAIN WILD-TYPE	299	26	109	11	4

Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S17. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
2Q GAIN MUTATED	43	7	10
2Q GAIN WILD-TYPE	115	79	156

Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S18. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
2Q GAIN MUTATED	54	13	7
2Q GAIN WILD-TYPE	170	137	138

Figure S18. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S19. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
2Q GAIN MUTATED	47	19	8
2Q GAIN WILD-TYPE	116	194	135

Figure S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S20. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
2Q GAIN MUTATED	14	53	8
2Q GAIN WILD-TYPE	127	166	147

Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S21. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
2Q GAIN MUTATED	6	45	7	17
2Q GAIN WILD-TYPE	49	117	109	165

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

Table S22. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
2Q GAIN MUTATED	6	37	15
2Q GAIN WILD-TYPE	115	140	79

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S23. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3P GAIN MUTATED	2	7	25	9	2
3P GAIN WILD-TYPE	303	41	129	3	3

Figure S23. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S24. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3P GAIN MUTATED	32	3	9
3P GAIN WILD-TYPE	192	147	136

Figure S24. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S25. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3Q GAIN MUTATED	5	9	52	10	2
3Q GAIN WILD-TYPE	300	39	102	2	3

Figure S25. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S26. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
3Q GAIN MUTATED	49	9	10
3Q GAIN WILD-TYPE	109	77	156

Figure S26. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S27. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3Q GAIN MUTATED	62	5	10
3Q GAIN WILD-TYPE	162	145	135

Figure S27. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S28. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
3Q GAIN MUTATED	51	18	8
3Q GAIN WILD-TYPE	112	195	135

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S29. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
3Q GAIN MUTATED	8	61	9
3Q GAIN WILD-TYPE	133	158	146

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S30. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
3Q GAIN MUTATED	0	50	9	19
3Q GAIN WILD-TYPE	55	112	107	163

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S31. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
4P GAIN MUTATED	0	1	12	0	0
4P GAIN WILD-TYPE	305	47	142	12	5

Figure S31. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S32. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5P GAIN MUTATED	3	5	40	0	1
5P GAIN WILD-TYPE	302	43	114	12	4

Figure S32. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S33. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
5P GAIN MUTATED	32	4	5
5P GAIN WILD-TYPE	126	82	161

Figure S33. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S34. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5P GAIN MUTATED	43	5	1
5P GAIN WILD-TYPE	181	145	144

Figure S34. 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 = 0.0089

Table S35. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
5P GAIN MUTATED	37	10	2
5P GAIN WILD-TYPE	126	203	141

Figure S35. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S36. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
5P GAIN MUTATED	9	38	1
5P GAIN WILD-TYPE	132	181	154

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S37. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
5P GAIN MUTATED	4	37	0	7
5P GAIN WILD-TYPE	51	125	116	175

Figure S37. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S38. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
5P GAIN MUTATED	2	30	7
5P GAIN WILD-TYPE	119	147	87

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S39. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
5P GAIN MUTATED	28	2	9
5P GAIN WILD-TYPE	143	106	104

Figure S39. 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 = 0.0089

Table S40. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5Q GAIN MUTATED	1	3	14	0	1
5Q GAIN WILD-TYPE	304	45	140	12	4

Figure S40. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S41. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5Q GAIN MUTATED	16	3	0
5Q GAIN WILD-TYPE	208	147	145

Figure S41. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S42. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6P GAIN MUTATED	6	5	57	7	1
6P GAIN WILD-TYPE	299	43	97	5	4

Figure S42. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S43. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
6P GAIN MUTATED	46	12	10
6P GAIN WILD-TYPE	112	74	156

Figure S43. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S44. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
6P GAIN MUTATED	57	5	14
6P GAIN WILD-TYPE	167	145	131

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S45. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
6P GAIN MUTATED	45	18	13
6P GAIN WILD-TYPE	118	195	130

Figure S45. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S46. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
6P GAIN MUTATED	10	55	11
6P GAIN WILD-TYPE	131	164	144

Figure S46. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S47. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
6P GAIN MUTATED	1	46	10	19
6P GAIN WILD-TYPE	54	116	106	163

Figure S47. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6Q GAIN MUTATED	5	5	43	7	1
6Q GAIN WILD-TYPE	300	43	111	5	4

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S49. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
6Q GAIN MUTATED	42	5	14
6Q GAIN WILD-TYPE	182	145	131

Figure S49. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.18

Table S50. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
6Q GAIN MUTATED	1	33	10	17
6Q GAIN WILD-TYPE	54	129	106	165

Figure S50. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S51. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7P GAIN MUTATED	8	24	27	4	1
7P GAIN WILD-TYPE	297	24	127	8	4

Figure S51. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S52. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7Q GAIN MUTATED	11	24	22	4	1
7Q GAIN WILD-TYPE	294	24	132	8	4

Figure S52. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S53. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8P GAIN MUTATED	39	22	41	12	2
8P GAIN WILD-TYPE	266	26	113	0	3

Figure S53. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S54. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8Q GAIN MUTATED	41	26	70	12	3
8Q GAIN WILD-TYPE	264	22	84	0	2

Figure S54. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.096

Table S55. Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S55. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S56. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
8Q GAIN MUTATED	90	29	33
8Q GAIN WILD-TYPE	134	121	112

Figure S56. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S57. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10P GAIN MUTATED	47	24	37	6	2
10P GAIN WILD-TYPE	258	24	117	6	3

Figure S57. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S58. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10Q GAIN MUTATED	46	23	33	5	2
10Q GAIN WILD-TYPE	259	25	121	7	3

Figure S58. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S59. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11P GAIN MUTATED	0	6	15	1	0
11P GAIN WILD-TYPE	305	42	139	11	5

Figure S59. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S60. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11Q GAIN MUTATED	0	6	12	1	0
11Q GAIN WILD-TYPE	305	42	142	11	5

Figure S60. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S61. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12P GAIN MUTATED	11	14	37	1	3
12P GAIN WILD-TYPE	294	34	117	11	2

Figure S61. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S62. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
12P GAIN MUTATED	31	14	7
12P GAIN WILD-TYPE	127	72	159

Figure S62. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S63. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
12P GAIN MUTATED	47	9	9
12P GAIN WILD-TYPE	177	141	136

Figure S63. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.044

Table S64. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
12P GAIN MUTATED	36	20	9
12P GAIN WILD-TYPE	127	193	134

Figure S64. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S65. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12Q GAIN MUTATED	11	13	24	1	3
12Q GAIN WILD-TYPE	294	35	130	11	2

Figure S65. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S66. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
13Q GAIN MUTATED	1	0	25	1	1
13Q GAIN WILD-TYPE	304	48	129	11	4

Figure S66. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S67. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
13Q GAIN MUTATED	16	7	1
13Q GAIN WILD-TYPE	142	79	165

Figure S67. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S68. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
13Q GAIN MUTATED	25	1	2
13Q GAIN WILD-TYPE	199	149	143

Figure S68. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S69. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
13Q GAIN MUTATED	25	1	2
13Q GAIN WILD-TYPE	138	212	141

Figure S69. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S70. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
13Q GAIN MUTATED	0	26	2
13Q GAIN WILD-TYPE	141	193	153

Figure S70. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S71. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
13Q GAIN MUTATED	0	24	2	2
13Q GAIN WILD-TYPE	55	138	114	180

Figure S71. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S72. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
14Q GAIN MUTATED	4	6	24	2	0
14Q GAIN WILD-TYPE	301	42	130	10	5

Figure S72. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S73. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
14Q GAIN MUTATED	28	1	6
14Q GAIN WILD-TYPE	196	149	139

Figure S73. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S74. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
14Q GAIN MUTATED	23	6	6
14Q GAIN WILD-TYPE	140	207	137

Figure S74. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.049

Table S75. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
14Q GAIN MUTATED	0	23	7	6
14Q GAIN WILD-TYPE	55	139	109	176

Figure S75. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S76. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
16P GAIN MUTATED	1	5	18	1	0
16P GAIN WILD-TYPE	304	43	136	11	5

Figure S76. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.22

Table S77. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17P GAIN MUTATED	1	1	8	1	1
17P GAIN WILD-TYPE	304	47	146	11	4

Figure S77. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S78. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17Q GAIN MUTATED	1	3	22	1	1
17Q GAIN WILD-TYPE	304	45	132	11	4

Figure S78. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S79. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
17Q GAIN MUTATED	21	2	2
17Q GAIN WILD-TYPE	137	84	164

Figure S79. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.075

Table S80. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
17Q GAIN MUTATED	23	2	3
17Q GAIN WILD-TYPE	201	148	142

Figure S80. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S81. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
17Q GAIN MUTATED	22	4	2
17Q GAIN WILD-TYPE	141	209	141

Figure S81. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.044

Table S82. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
17Q GAIN MUTATED	2	23	3
17Q GAIN WILD-TYPE	139	196	152

Figure S82. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S83. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18P GAIN MUTATED	3	5	59	1	0
18P GAIN WILD-TYPE	302	43	95	11	5

Figure S83. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S84. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
18P GAIN MUTATED	41	13	4
18P GAIN WILD-TYPE	117	73	162

Figure S84. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S85. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18P GAIN MUTATED	61	3	4
18P GAIN WILD-TYPE	163	147	141

Figure S85. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S86. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
18P GAIN MUTATED	56	8	4
18P GAIN WILD-TYPE	107	205	139

Figure S86. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S87. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
18P GAIN MUTATED	6	58	4
18P GAIN WILD-TYPE	135	161	151

Figure S87. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S88. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
18P GAIN MUTATED	2	55	3	8
18P GAIN WILD-TYPE	53	107	113	174

Figure S88. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S89. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
18P GAIN MUTATED	3	38	15
18P GAIN WILD-TYPE	118	139	79

Figure S89. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S90. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
18P GAIN MUTATED	34	3	19
18P GAIN WILD-TYPE	137	105	94

Figure S90. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S91. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18Q GAIN MUTATED	3	3	34	1	0
18Q GAIN WILD-TYPE	302	45	120	11	5

Figure S91. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S92. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
18Q GAIN MUTATED	25	7	3
18Q GAIN WILD-TYPE	133	79	163

Figure S92. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S93. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18Q GAIN MUTATED	36	2	3
18Q GAIN WILD-TYPE	188	148	142

Figure S93. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S94. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
18Q GAIN MUTATED	31	7	3
18Q GAIN WILD-TYPE	132	206	140

Figure S94. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S95. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
18Q GAIN MUTATED	6	33	2
18Q GAIN WILD-TYPE	135	186	153

Figure S95. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S96. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
18Q GAIN MUTATED	1	30	2	8
18Q GAIN WILD-TYPE	54	132	114	174

Figure S96. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S97. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
18Q GAIN MUTATED	1	25	7
18Q GAIN WILD-TYPE	120	152	87

Figure S97. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S98. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19P GAIN MUTATED	0	2	46	2	0
19P GAIN WILD-TYPE	305	46	108	10	5

Figure S98. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.13

Table S99. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
19P GAIN MUTATED	28	10	7
19P GAIN WILD-TYPE	130	76	159

Figure S99. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S100. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19P GAIN MUTATED	44	1	4
19P GAIN WILD-TYPE	180	149	141

Figure S100. 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 = 0.0089

Table S101. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
19P GAIN MUTATED	36	10	3
19P GAIN WILD-TYPE	127	203	140

Figure S101. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S102. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
19P GAIN MUTATED	3	42	5
19P GAIN WILD-TYPE	138	177	150

Figure S102. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S103. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
19P GAIN MUTATED	1	35	5	9
19P GAIN WILD-TYPE	54	127	111	173

Figure S103. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S104. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19Q GAIN MUTATED	0	3	50	2	0
19Q GAIN WILD-TYPE	305	45	104	10	5

Figure S104. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S105. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
19Q GAIN MUTATED	32	11	6
19Q GAIN WILD-TYPE	126	75	160

Figure S105. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S106. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19Q GAIN MUTATED	51	1	3
19Q GAIN WILD-TYPE	173	149	142

Figure S106. 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 = 0.0089

Table S107. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
19Q GAIN MUTATED	44	9	2
19Q GAIN WILD-TYPE	119	204	141

Figure S107. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S108. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
19Q GAIN MUTATED	4	47	4
19Q GAIN WILD-TYPE	137	172	151

Figure S108. 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 = 0.0089

Table S109. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
19Q GAIN MUTATED	1	43	4	7
19Q GAIN WILD-TYPE	54	119	112	175

Figure S109. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S110. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
20P GAIN MUTATED	6	22	76	1	2
20P GAIN WILD-TYPE	299	26	78	11	3

Figure S110. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S111. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
20P GAIN MUTATED	68	13	17
20P GAIN WILD-TYPE	90	73	149

Figure S111. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S112. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
20P GAIN MUTATED	84	9	14
20P GAIN WILD-TYPE	140	141	131

Figure S112. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S113. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
20P GAIN MUTATED	72	20	15
20P GAIN WILD-TYPE	91	193	128

Figure S113. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S114. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
20P GAIN MUTATED	13	79	14
20P GAIN WILD-TYPE	128	140	141

Figure S114. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S115. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
20P GAIN MUTATED	5	67	14	20
20P GAIN WILD-TYPE	50	95	102	162

Figure S115. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.044

Table S116. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
20P GAIN MUTATED	17	60	16
20P GAIN WILD-TYPE	104	117	78

Figure S116. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S117. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
20Q GAIN MUTATED	7	25	90	1	2
20Q GAIN WILD-TYPE	298	23	64	11	3

Figure S117. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S118. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
20Q GAIN MUTATED	76	16	21
20Q GAIN WILD-TYPE	82	70	145

Figure S118. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S119. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
20Q GAIN MUTATED	97	10	18
20Q GAIN WILD-TYPE	127	140	127

Figure S119. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S120. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
20Q GAIN MUTATED	83	23	19
20Q GAIN WILD-TYPE	80	190	124

Figure S120. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S121. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
20Q GAIN MUTATED	13	92	18
20Q GAIN WILD-TYPE	128	127	137

Figure S121. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S122. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
20Q GAIN MUTATED	6	77	16	24
20Q GAIN WILD-TYPE	49	85	100	158

Figure S122. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S123. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
20Q GAIN MUTATED	21	67	20
20Q GAIN WILD-TYPE	100	110	74

Figure S123. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S124. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
21Q GAIN MUTATED	1	2	32	1	0
21Q GAIN WILD-TYPE	304	46	122	11	5

Figure S124. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S125. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
21Q GAIN MUTATED	30	2	4
21Q GAIN WILD-TYPE	194	148	141

Figure S125. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S126. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
21Q GAIN MUTATED	28	4	4
21Q GAIN WILD-TYPE	135	209	139

Figure S126. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S127. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
21Q GAIN MUTATED	2	30	4
21Q GAIN WILD-TYPE	139	189	151

Figure S127. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S128. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
21Q GAIN MUTATED	1	28	3	4
21Q GAIN WILD-TYPE	54	134	113	178

Figure S128. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S129. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
22Q GAIN MUTATED	3	3	24	0	1
22Q GAIN WILD-TYPE	302	45	130	12	4

Figure S129. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S130. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
22Q GAIN MUTATED	26	1	1
22Q GAIN WILD-TYPE	132	85	165

Figure S130. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S131. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
22Q GAIN MUTATED	31	0	0
22Q GAIN WILD-TYPE	193	150	145

Figure S131. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S132. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
22Q GAIN MUTATED	28	3	0
22Q GAIN WILD-TYPE	135	210	143

Figure S132. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S133. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
22Q GAIN MUTATED	0	29	1
22Q GAIN WILD-TYPE	141	190	154

Figure S133. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S134. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
22Q GAIN MUTATED	0	26	2	2
22Q GAIN WILD-TYPE	55	136	114	180

Figure S134. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S135. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
22Q GAIN MUTATED	1	25	2
22Q GAIN WILD-TYPE	120	152	92

Figure S135. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S136. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
XQ GAIN MUTATED	10	19	23	9	2
XQ GAIN WILD-TYPE	295	29	131	3	3

Figure S136. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S137. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1P LOSS MUTATED	0	5	15	0	2
1P LOSS WILD-TYPE	305	43	139	12	3

Figure S137. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S138. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
1P LOSS MUTATED	17	1	0
1P LOSS WILD-TYPE	141	85	166

Figure S138. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S139. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1P LOSS MUTATED	20	1	1
1P LOSS WILD-TYPE	204	149	144

Figure S139. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S140. Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
1P LOSS MUTATED	17	5	0
1P LOSS WILD-TYPE	146	208	143

Figure S140. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S141. Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
1P LOSS MUTATED	2	19	1
1P LOSS WILD-TYPE	139	200	154

Figure S141. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S142. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
1P LOSS MUTATED	0	17	0	5
1P LOSS WILD-TYPE	55	145	116	177

Figure S142. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.049

Table S143. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
1Q LOSS MUTATED	0	2	11	0	0
1Q LOSS WILD-TYPE	305	46	143	12	5

Figure S143. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S144. Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
1Q LOSS MUTATED	11	0	0
1Q LOSS WILD-TYPE	147	86	166

Figure S144. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S145. Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
1Q LOSS MUTATED	13	0	0
1Q LOSS WILD-TYPE	211	150	145

Figure S145. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S146. Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
1Q LOSS MUTATED	11	2	0
1Q LOSS WILD-TYPE	152	211	143

Figure S146. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S147. Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
1Q LOSS MUTATED	0	13	0
1Q LOSS WILD-TYPE	141	206	155

Figure S147. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S148. Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
1Q LOSS MUTATED	0	12	0	1
1Q LOSS WILD-TYPE	55	150	116	181

Figure S148. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S149. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
2Q LOSS MUTATED	0	2	14	0	0
2Q LOSS WILD-TYPE	305	46	140	12	5

Figure S149. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S150. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3P LOSS MUTATED	0	5	44	0	1
3P LOSS WILD-TYPE	305	43	110	12	4

Figure S150. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S151. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
3P LOSS MUTATED	32	6	3
3P LOSS WILD-TYPE	126	80	163

Figure S151. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S152. Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3P LOSS MUTATED	46	1	2
3P LOSS WILD-TYPE	178	149	143

Figure S152. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S153. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
3P LOSS MUTATED	40	7	2
3P LOSS WILD-TYPE	123	206	141

Figure S153. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S154. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
3P LOSS MUTATED	6	39	3
3P LOSS WILD-TYPE	135	180	152

Figure S154. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S155. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
3P LOSS MUTATED	1	37	2	8
3P LOSS WILD-TYPE	54	125	114	174

Figure S155. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S156. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
3Q LOSS MUTATED	0	3	26	0	1
3Q LOSS WILD-TYPE	305	45	128	12	4

Figure S156. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S157. Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
3Q LOSS MUTATED	19	3	2
3Q LOSS WILD-TYPE	139	83	164

Figure S157. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S158. Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
3Q LOSS MUTATED	27	0	2
3Q LOSS WILD-TYPE	197	150	143

Figure S158. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S159. Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
3Q LOSS MUTATED	24	3	2
3Q LOSS WILD-TYPE	139	210	141

Figure S159. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S160. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
3Q LOSS MUTATED	1	24	3
3Q LOSS WILD-TYPE	140	195	152

Figure S160. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S161. Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
3Q LOSS MUTATED	0	22	2	4
3Q LOSS WILD-TYPE	55	140	114	178

Figure S161. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S162. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
4P LOSS MUTATED	4	11	82	1	2
4P LOSS WILD-TYPE	301	37	72	11	3

Figure S162. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S163. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
4P LOSS MUTATED	67	16	6
4P LOSS WILD-TYPE	91	70	160

Figure S163. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S164. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
4P LOSS MUTATED	87	6	7
4P LOSS WILD-TYPE	137	144	138

Figure S164. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S165. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
4P LOSS MUTATED	73	21	6
4P LOSS WILD-TYPE	90	192	137

Figure S165. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S166. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
4P LOSS MUTATED	8	81	9
4P LOSS WILD-TYPE	133	138	146

Figure S166. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S167. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
4P LOSS MUTATED	2	70	3	23
4P LOSS WILD-TYPE	53	92	113	159

Figure S167. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S168. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
4P LOSS MUTATED	10	55	24
4P LOSS WILD-TYPE	111	122	70

Figure S168. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S169. Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
4P LOSS MUTATED	53	9	27
4P LOSS WILD-TYPE	118	99	86

Figure S169. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S170. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
4Q LOSS MUTATED	3	10	83	1	2
4Q LOSS WILD-TYPE	302	38	71	11	3

Figure S170. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S171. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
4Q LOSS MUTATED	67	15	5
4Q LOSS WILD-TYPE	91	71	161

Figure S171. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S172. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
4Q LOSS MUTATED	86	7	6
4Q LOSS WILD-TYPE	138	143	139

Figure S172. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S173. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
4Q LOSS MUTATED	73	20	6
4Q LOSS WILD-TYPE	90	193	137

Figure S173. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S174. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
4Q LOSS MUTATED	8	80	9
4Q LOSS WILD-TYPE	133	139	146

Figure S174. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S175. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
4Q LOSS MUTATED	2	71	3	21
4Q LOSS WILD-TYPE	53	91	113	161

Figure S175. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S176. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
4Q LOSS MUTATED	9	52	26
4Q LOSS WILD-TYPE	112	125	68

Figure S176. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S177. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
4Q LOSS MUTATED	49	8	30
4Q LOSS WILD-TYPE	122	100	83

Figure S177. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S178. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5P LOSS MUTATED	0	9	43	1	1
5P LOSS WILD-TYPE	305	39	111	11	4

Figure S178. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S179. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
5P LOSS MUTATED	36	6	3
5P LOSS WILD-TYPE	122	80	163

Figure S179. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S180. Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5P LOSS MUTATED	45	4	5
5P LOSS WILD-TYPE	179	146	140

Figure S180. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S181. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
5P LOSS MUTATED	39	10	5
5P LOSS WILD-TYPE	124	203	138

Figure S181. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S182. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
5P LOSS MUTATED	5	42	7
5P LOSS WILD-TYPE	136	177	148

Figure S182. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S183. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
5P LOSS MUTATED	1	38	3	12
5P LOSS WILD-TYPE	54	124	113	170

Figure S183. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S184. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
5Q LOSS MUTATED	0	9	61	1	1
5Q LOSS WILD-TYPE	305	39	93	11	4

Figure S184. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S185. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
5Q LOSS MUTATED	51	6	3
5Q LOSS WILD-TYPE	107	80	163

Figure S185. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S186. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
5Q LOSS MUTATED	62	4	6
5Q LOSS WILD-TYPE	162	146	139

Figure S186. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S187. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
5Q LOSS MUTATED	54	11	7
5Q LOSS WILD-TYPE	109	202	136

Figure S187. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S188. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
5Q LOSS MUTATED	6	58	7
5Q LOSS WILD-TYPE	135	161	148

Figure S188. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S189. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
5Q LOSS MUTATED	1	52	4	14
5Q LOSS WILD-TYPE	54	110	112	168

Figure S189. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S190. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
5Q LOSS MUTATED	5	39	14
5Q LOSS WILD-TYPE	116	138	80

Figure S190. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S191. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6P LOSS MUTATED	0	3	14	0	0
6P LOSS WILD-TYPE	305	45	140	12	5

Figure S191. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S192. Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
6P LOSS MUTATED	14	3	0
6P LOSS WILD-TYPE	149	210	143

Figure S192. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S193. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
6Q LOSS MUTATED	0	3	21	0	0
6Q LOSS WILD-TYPE	305	45	133	12	5

Figure S193. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S194. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
6Q LOSS MUTATED	14	4	0
6Q LOSS WILD-TYPE	144	82	166

Figure S194. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S195. Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
6Q LOSS MUTATED	22	1	1
6Q LOSS WILD-TYPE	202	149	144

Figure S195. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S196. Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
6Q LOSS MUTATED	21	3	0
6Q LOSS WILD-TYPE	142	210	143

Figure S196. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S197. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
6Q LOSS MUTATED	0	17	0	5
6Q LOSS WILD-TYPE	55	145	116	177

Figure S197. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S198. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7P LOSS MUTATED	3	1	38	0	1
7P LOSS WILD-TYPE	302	47	116	12	4

Figure S198. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S199. Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
7P LOSS MUTATED	38	1	4
7P LOSS WILD-TYPE	186	149	141

Figure S199. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S200. Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
7P LOSS MUTATED	31	8	4
7P LOSS WILD-TYPE	132	205	139

Figure S200. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S201. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
7P LOSS MUTATED	2	34	7
7P LOSS WILD-TYPE	139	185	148

Figure S201. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S202. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
7P LOSS MUTATED	0	30	4	9
7P LOSS WILD-TYPE	55	132	112	173

Figure S202. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S203. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
7Q LOSS MUTATED	0	0	40	0	1
7Q LOSS WILD-TYPE	305	48	114	12	4

Figure S203. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S204. Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
7Q LOSS MUTATED	28	9	1
7Q LOSS WILD-TYPE	130	77	165

Figure S204. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S205. Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
7Q LOSS MUTATED	40	0	1
7Q LOSS WILD-TYPE	184	150	144

Figure S205. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S206. Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
7Q LOSS MUTATED	35	4	2
7Q LOSS WILD-TYPE	128	209	141

Figure S206. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S207. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
7Q LOSS MUTATED	1	37	3
7Q LOSS WILD-TYPE	140	182	152

Figure S207. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S208. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
7Q LOSS MUTATED	0	35	2	4
7Q LOSS WILD-TYPE	55	127	114	178

Figure S208. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S209. Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
8P LOSS MUTATED	0	5	0	0	0
8P LOSS WILD-TYPE	14	4	7	7	16

Figure S209. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S210. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8P LOSS MUTATED	4	3	67	0	1
8P LOSS WILD-TYPE	301	45	87	12	4

Figure S210. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S211. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
8P LOSS MUTATED	53	11	2
8P LOSS WILD-TYPE	105	75	164

Figure S211. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S212. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
8P LOSS MUTATED	68	3	3
8P LOSS WILD-TYPE	156	147	142

Figure S212. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S213. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
8P LOSS MUTATED	63	7	4
8P LOSS WILD-TYPE	100	206	139

Figure S213. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S214. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
8P LOSS MUTATED	2	66	4
8P LOSS WILD-TYPE	139	153	151

Figure S214. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S215. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
8P LOSS MUTATED	1	60	3	8
8P LOSS WILD-TYPE	54	102	113	174

Figure S215. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S216. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
8P LOSS MUTATED	3	41	18
8P LOSS WILD-TYPE	118	136	76

Figure S216. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S217. Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
8P LOSS MUTATED	37	4	21
8P LOSS WILD-TYPE	134	104	92

Figure S217. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S218. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
8Q LOSS MUTATED	1	1	23	0	0
8Q LOSS WILD-TYPE	304	47	131	12	5

Figure S218. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S219. Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
8Q LOSS MUTATED	20	3	0
8Q LOSS WILD-TYPE	138	83	166

Figure S219. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S220. Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
8Q LOSS MUTATED	23	0	2
8Q LOSS WILD-TYPE	201	150	143

Figure S220. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S221. Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
8Q LOSS MUTATED	22	1	2
8Q LOSS WILD-TYPE	141	212	141

Figure S221. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S222. Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
8Q LOSS MUTATED	0	22	2
8Q LOSS WILD-TYPE	141	197	153

Figure S222. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S223. Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
8Q LOSS MUTATED	0	21	2	1
8Q LOSS WILD-TYPE	55	141	114	181

Figure S223. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S224. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
9P LOSS MUTATED	2	7	0	0	0
9P LOSS WILD-TYPE	12	2	7	7	16

Figure S224. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S225. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
9P LOSS MUTATED	2	14	83	0	0
9P LOSS WILD-TYPE	303	34	71	12	5

Figure S225. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S226. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
9P LOSS MUTATED	55	20	9
9P LOSS WILD-TYPE	103	66	157

Figure S226. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S227. Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
9P LOSS MUTATED	80	6	13
9P LOSS WILD-TYPE	144	144	132

Figure S227. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S228. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
9P LOSS MUTATED	71	15	13
9P LOSS WILD-TYPE	92	198	130

Figure S228. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S229. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
9P LOSS MUTATED	9	72	15
9P LOSS WILD-TYPE	132	147	140

Figure S229. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S230. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
9P LOSS MUTATED	2	66	10	18
9P LOSS WILD-TYPE	53	96	106	164

Figure S230. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S231. Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9Q LOSS MUTATED	0	9	0	0
9Q LOSS WILD-TYPE	14	8	12	10

Figure S231. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S232. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
9Q LOSS MUTATED	2	7	0	0	0
9Q LOSS WILD-TYPE	12	2	7	7	16

Figure S232. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S233. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
9Q LOSS MUTATED	3	19	95	0	0
9Q LOSS WILD-TYPE	302	29	59	12	5

Figure S233. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S234. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
9Q LOSS MUTATED	66	22	13
9Q LOSS WILD-TYPE	92	64	153

Figure S234. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.16

Table S235. Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
9Q LOSS MUTATED	6	12	1	2	1	6
9Q LOSS WILD-TYPE	35	25	38	10	40	18

Figure S235. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S236. Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
9Q LOSS MUTATED	94	8	15
9Q LOSS WILD-TYPE	130	142	130

Figure S236. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S237. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
9Q LOSS MUTATED	82	20	15
9Q LOSS WILD-TYPE	81	193	128

Figure S237. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S238. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
9Q LOSS MUTATED	12	85	17
9Q LOSS WILD-TYPE	129	134	138

Figure S238. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S239. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
9Q LOSS MUTATED	2	75	11	26
9Q LOSS WILD-TYPE	53	87	105	156

Figure S239. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S240. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10P LOSS MUTATED	0	2	38	0	0
10P LOSS WILD-TYPE	305	46	116	12	5

Figure S240. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S241. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
10P LOSS MUTATED	28	5	1
10P LOSS WILD-TYPE	130	81	165

Figure S241. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S242. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
10P LOSS MUTATED	36	1	3
10P LOSS WILD-TYPE	188	149	142

Figure S242. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S243. Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
10P LOSS MUTATED	32	5	3
10P LOSS WILD-TYPE	131	208	140

Figure S243. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S244. Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
10P LOSS MUTATED	3	33	2
10P LOSS WILD-TYPE	138	186	153

Figure S244. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S245. Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
10P LOSS MUTATED	1	29	1	7
10P LOSS WILD-TYPE	54	133	115	175

Figure S245. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S246. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
10Q LOSS MUTATED	1	2	36	0	0
10Q LOSS WILD-TYPE	304	46	118	12	5

Figure S246. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S247. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
10Q LOSS MUTATED	27	6	1
10Q LOSS WILD-TYPE	131	80	165

Figure S247. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S248. Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
10Q LOSS MUTATED	34	1	4
10Q LOSS WILD-TYPE	190	149	141

Figure S248. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S249. Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
10Q LOSS MUTATED	28	7	4
10Q LOSS WILD-TYPE	135	206	139

Figure S249. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S250. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
10Q LOSS MUTATED	4	31	3
10Q LOSS WILD-TYPE	137	188	152

Figure S250. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S251. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
10Q LOSS MUTATED	1	27	2	8
10Q LOSS WILD-TYPE	54	135	114	174

Figure S251. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S252. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11P LOSS MUTATED	1	9	60	0	2
11P LOSS WILD-TYPE	304	39	94	12	3

Figure S252. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S253. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
11P LOSS MUTATED	50	12	5
11P LOSS WILD-TYPE	108	74	161

Figure S253. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S254. Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
11P LOSS MUTATED	62	4	6
11P LOSS WILD-TYPE	162	146	139

Figure S254. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S255. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
11P LOSS MUTATED	52	13	7
11P LOSS WILD-TYPE	111	200	136

Figure S255. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S256. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
11P LOSS MUTATED	7	56	8
11P LOSS WILD-TYPE	134	163	147

Figure S256. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S257. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
11P LOSS MUTATED	0	48	6	17
11P LOSS WILD-TYPE	55	114	110	165

Figure S257. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S258. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
11Q LOSS MUTATED	1	11	54	0	2
11Q LOSS WILD-TYPE	304	37	100	12	3

Figure S258. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S259. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
11Q LOSS MUTATED	48	11	6
11Q LOSS WILD-TYPE	110	75	160

Figure S259. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S260. Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
11Q LOSS MUTATED	56	4	8
11Q LOSS WILD-TYPE	168	146	137

Figure S260. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S261. Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
11Q LOSS MUTATED	50	10	8
11Q LOSS WILD-TYPE	113	203	135

Figure S261. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S262. Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
11Q LOSS MUTATED	7	52	9
11Q LOSS WILD-TYPE	134	167	146

Figure S262. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S263. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
11Q LOSS MUTATED	0	46	7	15
11Q LOSS WILD-TYPE	55	116	109	167

Figure S263. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.16

Table S264. Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
11Q LOSS MUTATED	10	44	11
11Q LOSS WILD-TYPE	111	133	83

Figure S264. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.23

Table S265. Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
11Q LOSS MUTATED	43	10	12
11Q LOSS WILD-TYPE	128	98	101

Figure S265. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S266. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12P LOSS MUTATED	0	3	38	1	0
12P LOSS WILD-TYPE	305	45	116	11	5

Figure S266. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S267. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
12P LOSS MUTATED	28	3	4
12P LOSS WILD-TYPE	130	83	162

Figure S267. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S268. Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
12P LOSS MUTATED	37	0	5
12P LOSS WILD-TYPE	187	150	140

Figure S268. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S269. Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
12P LOSS MUTATED	33	3	6
12P LOSS WILD-TYPE	130	210	137

Figure S269. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S270. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
12P LOSS MUTATED	2	33	5
12P LOSS WILD-TYPE	139	186	150

Figure S270. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S271. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
12P LOSS MUTATED	0	32	3	5
12P LOSS WILD-TYPE	55	130	113	177

Figure S271. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S272. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
12Q LOSS MUTATED	0	2	31	1	0
12Q LOSS WILD-TYPE	305	46	123	11	5

Figure S272. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S273. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
12Q LOSS MUTATED	25	1	2
12Q LOSS WILD-TYPE	133	85	164

Figure S273. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S274. Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
12Q LOSS MUTATED	31	0	3
12Q LOSS WILD-TYPE	193	150	142

Figure S274. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S275. Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
12Q LOSS MUTATED	29	1	4
12Q LOSS WILD-TYPE	134	212	139

Figure S275. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S276. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
12Q LOSS MUTATED	3	26	3
12Q LOSS WILD-TYPE	138	193	152

Figure S276. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S277. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
12Q LOSS MUTATED	0	28	1	3
12Q LOSS WILD-TYPE	55	134	115	179

Figure S277. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S278. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
13Q LOSS MUTATED	4	20	63	1	1
13Q LOSS WILD-TYPE	301	28	91	11	4

Figure S278. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S279. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
13Q LOSS MUTATED	48	17	12
13Q LOSS WILD-TYPE	110	69	154

Figure S279. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S280. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
13Q LOSS MUTATED	65	8	16
13Q LOSS WILD-TYPE	159	142	129

Figure S280. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S281. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
13Q LOSS MUTATED	49	25	15
13Q LOSS WILD-TYPE	114	188	128

Figure S281. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S282. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
13Q LOSS MUTATED	16	58	14
13Q LOSS WILD-TYPE	125	161	141

Figure S282. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S283. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
13Q LOSS MUTATED	2	49	9	28
13Q LOSS WILD-TYPE	53	113	107	154

Figure S283. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S284. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
14Q LOSS MUTATED	0	4	49	1	2
14Q LOSS WILD-TYPE	305	44	105	11	3

Figure S284. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S285. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
14Q LOSS MUTATED	36	7	1
14Q LOSS WILD-TYPE	122	79	165

Figure S285. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S286. Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
14Q LOSS MUTATED	49	3	4
14Q LOSS WILD-TYPE	175	147	141

Figure S286. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S287. Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
14Q LOSS MUTATED	44	8	4
14Q LOSS WILD-TYPE	119	205	139

Figure S287. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S288. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
14Q LOSS MUTATED	7	44	3
14Q LOSS WILD-TYPE	134	175	152

Figure S288. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S289. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
14Q LOSS MUTATED	0	40	1	13
14Q LOSS WILD-TYPE	55	122	115	169

Figure S289. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S290. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
14Q LOSS MUTATED	3	34	8
14Q LOSS WILD-TYPE	118	143	86

Figure S290. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S291. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
15Q LOSS MUTATED	1	6	0	0	0
15Q LOSS WILD-TYPE	13	3	7	7	16

Figure S291. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S292. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
15Q LOSS MUTATED	4	14	86	0	2
15Q LOSS WILD-TYPE	301	34	68	12	3

Figure S292. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S293. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
15Q LOSS MUTATED	67	18	8
15Q LOSS WILD-TYPE	91	68	158

Figure S293. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S294. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
15Q LOSS MUTATED	91	7	8
15Q LOSS WILD-TYPE	133	143	137

Figure S294. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S295. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
15Q LOSS MUTATED	77	21	8
15Q LOSS WILD-TYPE	86	192	135

Figure S295. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S296. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
15Q LOSS MUTATED	11	84	9
15Q LOSS WILD-TYPE	130	135	146

Figure S296. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S297. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
15Q LOSS MUTATED	0	71	5	28
15Q LOSS WILD-TYPE	55	91	111	154

Figure S297. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S298. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
15Q LOSS MUTATED	10	62	20
15Q LOSS WILD-TYPE	111	115	74

Figure S298. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S299. Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
15Q LOSS MUTATED	59	10	23
15Q LOSS WILD-TYPE	112	98	90

Figure S299. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S300. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
16P LOSS MUTATED	5	9	80	0	0
16P LOSS WILD-TYPE	300	39	74	12	5

Figure S300. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S301. Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
16P LOSS MUTATED	58	20	6
16P LOSS WILD-TYPE	100	66	160

Figure S301. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S302. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
16P LOSS MUTATED	82	5	7
16P LOSS WILD-TYPE	142	145	138

Figure S302. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S303. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
16P LOSS MUTATED	67	19	8
16P LOSS WILD-TYPE	96	194	135

Figure S303. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S304. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
16P LOSS MUTATED	10	72	9
16P LOSS WILD-TYPE	131	147	146

Figure S304. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S305. Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
16P LOSS MUTATED	1	65	7	18
16P LOSS WILD-TYPE	54	97	109	164

Figure S305. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S306. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
16P LOSS MUTATED	10	48	25
16P LOSS WILD-TYPE	111	129	69

Figure S306. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S307. Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
16P LOSS MUTATED	45	9	29
16P LOSS WILD-TYPE	126	99	84

Figure S307. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S308. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
16Q LOSS MUTATED	15	13	107	0	0
16Q LOSS WILD-TYPE	290	35	47	12	5

Figure S308. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S309. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
16Q LOSS MUTATED	77	26	15
16Q LOSS WILD-TYPE	81	60	151

Figure S309. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S310. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
16Q LOSS MUTATED	107	15	13
16Q LOSS WILD-TYPE	117	135	132

Figure S310. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S311. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
16Q LOSS MUTATED	89	33	13
16Q LOSS WILD-TYPE	74	180	130

Figure S311. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S312. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
16Q LOSS MUTATED	20	96	15
16Q LOSS WILD-TYPE	121	123	140

Figure S312. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S313. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
16Q LOSS MUTATED	7	84	11	29
16Q LOSS WILD-TYPE	48	78	105	153

Figure S313. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S314. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
16Q LOSS MUTATED	16	68	32
16Q LOSS WILD-TYPE	105	109	62

Figure S314. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S315. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
16Q LOSS MUTATED	65	15	36
16Q LOSS WILD-TYPE	106	93	77

Figure S315. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S316. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
17P LOSS MUTATED	1	6	1	0	0
17P LOSS WILD-TYPE	13	3	6	7	16

Figure S316. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S317. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17P LOSS MUTATED	3	12	107	0	0
17P LOSS WILD-TYPE	302	36	47	12	5

Figure S317. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S318. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
17P LOSS MUTATED	76	20	11
17P LOSS WILD-TYPE	82	66	155

Figure S318. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S319. Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
17P LOSS MUTATED	102	5	14
17P LOSS WILD-TYPE	122	145	131

Figure S319. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S320. Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
17P LOSS MUTATED	86	19	16
17P LOSS WILD-TYPE	77	194	127

Figure S320. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S321. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
17P LOSS MUTATED	8	94	17
17P LOSS WILD-TYPE	133	125	138

Figure S321. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S322. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
17P LOSS MUTATED	1	80	12	26
17P LOSS WILD-TYPE	54	82	104	156

Figure S322. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S323. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
17Q LOSS MUTATED	0	6	0	0	0
17Q LOSS WILD-TYPE	14	3	7	7	16

Figure S323. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S324. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
17Q LOSS MUTATED	2	11	75	0	0
17Q LOSS WILD-TYPE	303	37	79	12	5

Figure S324. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S325. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
17Q LOSS MUTATED	50	17	10
17Q LOSS WILD-TYPE	108	69	156

Figure S325. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S326. Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
17Q LOSS MUTATED	70	5	12
17Q LOSS WILD-TYPE	154	145	133

Figure S326. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S327. Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
17Q LOSS MUTATED	56	17	14
17Q LOSS WILD-TYPE	107	196	129

Figure S327. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S328. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
17Q LOSS MUTATED	8	62	15
17Q LOSS WILD-TYPE	133	157	140

Figure S328. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S329. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
17Q LOSS MUTATED	1	52	9	23
17Q LOSS WILD-TYPE	54	110	107	159

Figure S329. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S330. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18P LOSS MUTATED	1	11	38	0	2
18P LOSS WILD-TYPE	304	37	116	12	3

Figure S330. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S331. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
18P LOSS MUTATED	34	8	4
18P LOSS WILD-TYPE	124	78	162

Figure S331. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S332. Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18P LOSS MUTATED	40	6	6
18P LOSS WILD-TYPE	184	144	139

Figure S332. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.07

Table S333. Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
18P LOSS MUTATED	8	36	7
18P LOSS WILD-TYPE	133	183	148

Figure S333. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S334. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
18P LOSS MUTATED	1	27	4	19
18P LOSS WILD-TYPE	54	135	112	163

Figure S334. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S335. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
18Q LOSS MUTATED	1	13	49	0	2
18Q LOSS WILD-TYPE	304	35	105	12	3

Figure S335. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S336. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
18Q LOSS MUTATED	42	11	6
18Q LOSS WILD-TYPE	116	75	160

Figure S336. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S337. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
18Q LOSS MUTATED	52	6	7
18Q LOSS WILD-TYPE	172	144	138

Figure S337. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S338. Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
18Q LOSS MUTATED	38	19	8
18Q LOSS WILD-TYPE	125	194	135

Figure S338. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S339. Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
18Q LOSS MUTATED	7	48	9
18Q LOSS WILD-TYPE	134	171	146

Figure S339. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S340. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
18Q LOSS MUTATED	0	39	5	20
18Q LOSS WILD-TYPE	55	123	111	162

Figure S340. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S341. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19P LOSS MUTATED	1	13	43	0	0
19P LOSS WILD-TYPE	304	35	111	12	5

Figure S341. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S342. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
19P LOSS MUTATED	42	7	2
19P LOSS WILD-TYPE	116	79	164

Figure S342. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S343. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19P LOSS MUTATED	48	5	4
19P LOSS WILD-TYPE	176	145	141

Figure S343. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S344. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
19P LOSS MUTATED	41	12	4
19P LOSS WILD-TYPE	122	201	139

Figure S344. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S345. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
19P LOSS MUTATED	5	44	6
19P LOSS WILD-TYPE	136	175	149

Figure S345. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S346. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
19P LOSS MUTATED	1	37	4	13
19P LOSS WILD-TYPE	54	125	112	169

Figure S346. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S347. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
19P LOSS MUTATED	5	38	7
19P LOSS WILD-TYPE	116	139	87

Figure S347. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.08

Table S348. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
19P LOSS MUTATED	35	5	10
19P LOSS WILD-TYPE	136	103	103

Figure S348. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S349. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
19Q LOSS MUTATED	2	12	39	0	0
19Q LOSS WILD-TYPE	303	36	115	12	5

Figure S349. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S350. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
19Q LOSS MUTATED	34	8	4
19Q LOSS WILD-TYPE	124	78	162

Figure S350. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S351. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
19Q LOSS MUTATED	42	5	5
19Q LOSS WILD-TYPE	182	145	140

Figure S351. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S352. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
19Q LOSS MUTATED	37	10	5
19Q LOSS WILD-TYPE	126	203	138

Figure S352. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S353. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
19Q LOSS MUTATED	5	39	7
19Q LOSS WILD-TYPE	136	180	148

Figure S353. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S354. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
19Q LOSS MUTATED	1	32	5	13
19Q LOSS WILD-TYPE	54	130	111	169

Figure S354. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S355. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
20P LOSS MUTATED	1	4	13	0	0
20P LOSS WILD-TYPE	304	44	141	12	5

Figure S355. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S356. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
21Q LOSS MUTATED	4	6	41	0	2
21Q LOSS WILD-TYPE	301	42	113	12	3

Figure S356. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S357. Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
21Q LOSS MUTATED	32	7	5
21Q LOSS WILD-TYPE	126	79	161

Figure S357. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S358. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
21Q LOSS MUTATED	45	7	1
21Q LOSS WILD-TYPE	179	143	144

Figure S358. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S359. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
21Q LOSS MUTATED	36	15	2
21Q LOSS WILD-TYPE	127	198	141

Figure S359. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S360. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
21Q LOSS MUTATED	6	43	2
21Q LOSS WILD-TYPE	135	176	153

Figure S360. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S361. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
21Q LOSS MUTATED	2	35	2	12
21Q LOSS WILD-TYPE	53	127	114	170

Figure S361. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S362. Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
21Q LOSS MUTATED	1	34	9
21Q LOSS WILD-TYPE	120	143	85

Figure S362. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S363. Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
21Q LOSS MUTATED	28	2	14
21Q LOSS WILD-TYPE	143	106	99

Figure S363. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S364. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
22Q LOSS MUTATED	3	14	87	0	1
22Q LOSS WILD-TYPE	302	34	67	12	4

Figure S364. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S365. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
22Q LOSS MUTATED	63	20	13
22Q LOSS WILD-TYPE	95	66	153

Figure S365. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S366. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
22Q LOSS MUTATED	81	7	16
22Q LOSS WILD-TYPE	143	143	129

Figure S366. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S367. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
22Q LOSS MUTATED	65	23	16
22Q LOSS WILD-TYPE	98	190	127

Figure S367. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S368. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
22Q LOSS MUTATED	10	76	17
22Q LOSS WILD-TYPE	131	143	138

Figure S368. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S369. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
22Q LOSS MUTATED	1	64	11	27
22Q LOSS WILD-TYPE	54	98	105	155

Figure S369. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S370. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
XQ LOSS MUTATED	1	7	61	0	0
XQ LOSS WILD-TYPE	304	41	93	12	5

Figure S370. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S371. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
XQ LOSS MUTATED	41	11	6
XQ LOSS WILD-TYPE	117	75	160

Figure S371. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.09

Table S372. Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
XQ LOSS MUTATED	3	13	2	1	1	1
XQ LOSS WILD-TYPE	38	24	37	11	40	23

Figure S372. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S373. Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
XQ LOSS MUTATED	59	5	4
XQ LOSS WILD-TYPE	165	145	141

Figure S373. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S374. Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
XQ LOSS MUTATED	46	17	5
XQ LOSS WILD-TYPE	117	196	138

Figure S374. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S375. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
XQ LOSS MUTATED	7	50	9
XQ LOSS WILD-TYPE	134	169	146

Figure S375. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S376. Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
XQ LOSS MUTATED	1	45	4	16
XQ LOSS WILD-TYPE	54	117	112	166

Figure S376. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S377. Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
XQ LOSS MUTATED	42	5	11
XQ LOSS WILD-TYPE	129	103	102

Figure S377. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 524
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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