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

Stomach Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1PZ57S1

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 79 arm-level events and 10 molecular subtypes across 441 patients, 186 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 186 significant findings detected.


		Clinical Features	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
20q gain	279 (63%)	162	1e-05 (0.0079)	1e-05 (0.0079)	0.0524 (1.00)	0.228 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	2e-05 (0.0136)	0.111 (1.00)
5q loss	106 (24%)	335	1e-05 (0.0079)	1e-05 (0.0079)	0.479 (1.00)	0.953 (1.00)	2e-05 (0.0136)	3e-05 (0.02)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	0.00334 (1.00)
9p loss	150 (34%)	291	1e-05 (0.0079)	1e-05 (0.0079)	0.00211 (1.00)	0.00029 (0.177)	1e-05 (0.0079)	0.00026 (0.161)	2e-05 (0.0136)	1e-05 (0.0079)	0.021 (1.00)	0.0658 (1.00)
16p loss	100 (23%)	341	1e-05 (0.0079)	5e-05 (0.0327)	0.712 (1.00)	0.883 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	0.15 (1.00)
16q loss	115 (26%)	326	1e-05 (0.0079)	1e-05 (0.0079)	0.0392 (1.00)	0.089 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	0.0001 (0.0634)	0.494 (1.00)
19p loss	115 (26%)	326	1e-05 (0.0079)	1e-05 (0.0079)	0.00656 (1.00)	0.107 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	1e-05 (0.0079)	6e-05 (0.0388)	0.00698 (1.00)
19q loss	87 (20%)	354	1e-05 (0.0079)	1e-05 (0.0079)	0.03 (1.00)	0.205 (1.00)	1e-05 (0.0079)	5e-05 (0.0327)	1e-05 (0.0079)	1e-05 (0.0079)	0.00026 (0.161)	0.0129 (1.00)
20p gain	243 (55%)	198	1e-05 (0.0079)	0.00018 (0.112)	0.0781 (1.00)	0.194 (1.00)	0.00052 (0.311)	1e-05 (0.0079)	1e-05 (0.0079)	2e-05 (0.0136)	5e-05 (0.0327)	0.554 (1.00)
4p loss	167 (38%)	274	1e-05 (0.0079)	8e-05 (0.051)	0.287 (1.00)	0.138 (1.00)	0.0006 (0.356)	0.00017 (0.106)	1e-05 (0.0079)	1e-05 (0.0079)	0.00035 (0.213)	0.245 (1.00)
12p loss	63 (14%)	378	1e-05 (0.0079)	1e-05 (0.0079)	0.219 (1.00)	0.137 (1.00)	2e-05 (0.0136)	1e-05 (0.0079)	8e-05 (0.051)	2e-05 (0.0136)	0.0968 (1.00)	0.0324 (1.00)
17p loss	164 (37%)	277	1e-05 (0.0079)	1e-05 (0.0079)	0.58 (1.00)	0.0272 (1.00)	3e-05 (0.02)	1e-05 (0.0079)	1e-05 (0.0079)	2e-05 (0.0136)	0.115 (1.00)	0.00068 (0.401)
5p gain	102 (23%)	339	1e-05 (0.0079)	7e-05 (0.0451)	0.262 (1.00)	0.96 (1.00)	1e-05 (0.0079)	0.00535 (1.00)	0.0002 (0.124)	1e-05 (0.0079)	0.00868 (1.00)	0.019 (1.00)
6q gain	64 (15%)	377	1e-05 (0.0079)	1e-05 (0.0079)	0.0653 (1.00)	0.342 (1.00)	0.00032 (0.195)	0.0228 (1.00)	7e-05 (0.0451)	1e-05 (0.0079)	0.00101 (0.586)	0.00349 (1.00)
9q loss	104 (24%)	337	1e-05 (0.0079)	0.00026 (0.161)	0.208 (1.00)	0.0158 (1.00)	4e-05 (0.0263)	0.0095 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	0.0132 (1.00)	0.192 (1.00)
6p gain	78 (18%)	363	1e-05 (0.0079)	1e-05 (0.0079)	0.108 (1.00)	0.347 (1.00)	0.00063 (0.374)	0.00766 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	0.00139 (0.791)	0.00156 (0.877)
13q gain	154 (35%)	287	1e-05 (0.0079)	0.00014 (0.0881)	0.677 (1.00)	0.608 (1.00)	0.0228 (1.00)	8e-05 (0.051)	0.00095 (0.554)	0.00012 (0.076)	0.00134 (0.765)	0.529 (1.00)
18p gain	84 (19%)	357	1e-05 (0.0079)	1e-05 (0.0079)	0.104 (1.00)	0.0505 (1.00)	0.00877 (1.00)	0.00151 (0.853)	0.00024 (0.149)	2e-05 (0.0136)	0.00406 (1.00)	0.0111 (1.00)
4q loss	164 (37%)	277	1e-05 (0.0079)	5e-05 (0.0327)	0.0802 (1.00)	0.032 (1.00)	0.006 (1.00)	0.00148 (0.839)	3e-05 (0.02)	1e-05 (0.0079)	0.00558 (1.00)	0.21 (1.00)
10q loss	67 (15%)	374	1e-05 (0.0079)	0.00031 (0.189)	0.676 (1.00)	0.0516 (1.00)	0.00187 (1.00)	0.00212 (1.00)	3e-05 (0.02)	0.00016 (0.1)	0.275 (1.00)	0.205 (1.00)
14q loss	111 (25%)	330	1e-05 (0.0079)	2e-05 (0.0136)	0.56 (1.00)	0.531 (1.00)	0.00106 (0.614)	0.00901 (1.00)	4e-05 (0.0263)	9e-05 (0.0571)	0.139 (1.00)	0.0587 (1.00)
22q loss	146 (33%)	295	1e-05 (0.0079)	1e-05 (0.0079)	0.0158 (1.00)	0.0071 (1.00)	0.00113 (0.652)	0.00421 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	0.00146 (0.829)	0.0892 (1.00)
1q gain	103 (23%)	338	1e-05 (0.0079)	0.00047 (0.283)	0.0582 (1.00)	0.222 (1.00)	3e-05 (0.02)	0.00206 (1.00)	0.00064 (0.379)	3e-05 (0.02)	0.00359 (1.00)	0.298 (1.00)
11q gain	74 (17%)	367	1e-05 (0.0079)	0.00169 (0.943)	0.835 (1.00)	1 (1.00)	0.313 (1.00)	0.0057 (1.00)	1e-05 (0.0079)	0.00037 (0.224)	0.012 (1.00)	0.00918 (1.00)
21q gain	21 (5%)	420	0.00016 (0.1)	0.00036 (0.219)	0.145 (1.00)	0.636 (1.00)	0.00992 (1.00)	0.0316 (1.00)	0.091 (1.00)	7e-05 (0.0451)	0.168 (1.00)	0.0297 (1.00)
3q loss	54 (12%)	387	1e-05 (0.0079)	0.00049 (0.294)	0.193 (1.00)	0.277 (1.00)	1e-05 (0.0079)	1e-05 (0.0079)	0.0275 (1.00)	0.0124 (1.00)	0.0824 (1.00)	0.00134 (0.765)
5p loss	60 (14%)	381	1e-05 (0.0079)	0.00043 (0.259)	0.221 (1.00)	0.755 (1.00)	0.00229 (1.00)	0.0124 (1.00)	0.00028 (0.172)	7e-05 (0.0451)	0.00351 (1.00)	0.15 (1.00)
10p loss	64 (15%)	377	1e-05 (0.0079)	0.00576 (1.00)	0.709 (1.00)	0.0946 (1.00)	0.0147 (1.00)	0.0746 (1.00)	5e-05 (0.0327)	0.00032 (0.195)	0.212 (1.00)	0.353 (1.00)
17q loss	74 (17%)	367	1e-05 (0.0079)	2e-05 (0.0136)	0.265 (1.00)	0.0334 (1.00)	0.00285 (1.00)	0.00799 (1.00)	0.00042 (0.254)	0.0002 (0.124)	0.113 (1.00)	0.637 (1.00)
2p gain	77 (17%)	364	1e-05 (0.0079)	0.00414 (1.00)	0.0214 (1.00)	0.117 (1.00)	0.142 (1.00)	0.0284 (1.00)	0.00028 (0.172)	0.00738 (1.00)	0.142 (1.00)	0.0244 (1.00)
10p gain	98 (22%)	343	1e-05 (0.0079)	0.00013 (0.082)	0.132 (1.00)	0.53 (1.00)	0.00149 (0.843)	0.146 (1.00)	0.15 (1.00)	0.00345 (1.00)	0.227 (1.00)	0.416 (1.00)
11p gain	64 (15%)	377	1e-05 (0.0079)	0.037 (1.00)	0.934 (1.00)	0.846 (1.00)	0.284 (1.00)	0.395 (1.00)	6e-05 (0.0388)	0.00154 (0.869)	0.0395 (1.00)	0.123 (1.00)
1p loss	59 (13%)	382	1e-05 (0.0079)	1e-05 (0.0079)	0.0309 (1.00)	0.191 (1.00)	0.0715 (1.00)	0.0078 (1.00)	0.00844 (1.00)	0.00421 (1.00)	0.00776 (1.00)	0.432 (1.00)
1q loss	28 (6%)	413	3e-05 (0.02)	1e-05 (0.0079)	0.0341 (1.00)	0.298 (1.00)	0.593 (1.00)	0.152 (1.00)	0.0744 (1.00)	0.314 (1.00)	0.521 (1.00)	0.553 (1.00)
2q loss	33 (7%)	408	1e-05 (0.0079)	7e-05 (0.0451)	0.665 (1.00)	0.803 (1.00)	0.00886 (1.00)	0.262 (1.00)	0.0234 (1.00)	0.0327 (1.00)	0.607 (1.00)	0.207 (1.00)
3p loss	91 (21%)	350	1e-05 (0.0079)	0.00346 (1.00)	0.358 (1.00)	0.2 (1.00)	0.00309 (1.00)	0.00026 (0.161)	0.00163 (0.913)	0.00106 (0.614)	0.157 (1.00)	0.021 (1.00)
7p loss	20 (5%)	421	0.0004 (0.242)	0.0204 (1.00)	0.443 (1.00)	0.432 (1.00)	0.00165 (0.922)	0.339 (1.00)	0.00022 (0.136)	0.0224 (1.00)	0.00224 (1.00)	0.22 (1.00)
8p loss	88 (20%)	353	1e-05 (0.0079)	0.0689 (1.00)	0.394 (1.00)	0.645 (1.00)	0.0172 (1.00)	0.00126 (0.724)	0.00218 (1.00)	0.00721 (1.00)	0.0193 (1.00)	2e-05 (0.0136)
12q loss	52 (12%)	389	1e-05 (0.0079)	1e-05 (0.0079)	0.277 (1.00)	0.111 (1.00)	0.00054 (0.322)	0.0008 (0.469)	0.0757 (1.00)	0.00099 (0.575)	0.371 (1.00)	0.198 (1.00)
15q loss	90 (20%)	351	1e-05 (0.0079)	0.00126 (0.724)	0.00552 (1.00)	0.526 (1.00)	0.00012 (0.076)	0.00176 (0.979)	0.0243 (1.00)	0.0201 (1.00)	0.15 (1.00)	0.00335 (1.00)
18q loss	154 (35%)	287	1e-05 (0.0079)	0.0607 (1.00)	0.341 (1.00)	0.813 (1.00)	0.0213 (1.00)	0.0254 (1.00)	0.00013 (0.082)	0.00068 (0.401)	0.0442 (1.00)	0.0228 (1.00)
xq loss	51 (12%)	390	1e-05 (0.0079)	5e-05 (0.0327)	0.504 (1.00)	0.111 (1.00)	0.0734 (1.00)	0.0929 (1.00)	0.0704 (1.00)	0.252 (1.00)	0.0781 (1.00)	0.0639 (1.00)
1p gain	51 (12%)	390	1e-05 (0.0079)	0.0934 (1.00)	0.00249 (1.00)	0.406 (1.00)	0.00155 (0.873)	0.124 (1.00)	0.00064 (0.379)	0.00377 (1.00)	0.0753 (1.00)	0.063 (1.00)
2q gain	66 (15%)	375	1e-05 (0.0079)	0.122 (1.00)	0.237 (1.00)	0.552 (1.00)	0.0444 (1.00)	0.0298 (1.00)	0.00092 (0.537)	0.0681 (1.00)	0.0331 (1.00)	0.286 (1.00)
3q gain	93 (21%)	348	1e-05 (0.0079)	0.318 (1.00)	0.875 (1.00)	0.151 (1.00)	0.141 (1.00)	0.0204 (1.00)	0.0558 (1.00)	0.338 (1.00)	0.0965 (1.00)	0.0191 (1.00)
7p gain	197 (45%)	244	1e-05 (0.0079)	0.00198 (1.00)	0.676 (1.00)	0.495 (1.00)	0.341 (1.00)	0.00051 (0.305)	0.223 (1.00)	0.028 (1.00)	0.365 (1.00)	0.00324 (1.00)
7q gain	169 (38%)	272	1e-05 (0.0079)	0.0551 (1.00)	0.924 (1.00)	0.437 (1.00)	0.338 (1.00)	0.00172 (0.958)	0.315 (1.00)	0.179 (1.00)	0.54 (1.00)	0.0424 (1.00)
8p gain	182 (41%)	259	3e-05 (0.02)	0.0157 (1.00)	0.603 (1.00)	0.241 (1.00)	0.446 (1.00)	0.104 (1.00)	0.205 (1.00)	0.404 (1.00)	0.455 (1.00)	0.318 (1.00)
10q gain	70 (16%)	371	1e-05 (0.0079)	0.0393 (1.00)	0.124 (1.00)	0.854 (1.00)	0.013 (1.00)	0.122 (1.00)	0.465 (1.00)	0.337 (1.00)	0.676 (1.00)	0.447 (1.00)
12p gain	90 (20%)	351	0.00016 (0.1)	0.177 (1.00)	0.237 (1.00)	0.337 (1.00)	0.167 (1.00)	0.102 (1.00)	0.0578 (1.00)	0.174 (1.00)	0.129 (1.00)	0.0836 (1.00)
14q gain	29 (7%)	412	7e-05 (0.0451)	0.0846 (1.00)	0.812 (1.00)	0.929 (1.00)	0.196 (1.00)	0.763 (1.00)	0.00767 (1.00)	0.51 (1.00)	0.205 (1.00)	0.596 (1.00)
15q gain	39 (9%)	402	5e-05 (0.0327)	0.00324 (1.00)	0.347 (1.00)	0.828 (1.00)	0.035 (1.00)	0.226 (1.00)	0.116 (1.00)	0.00885 (1.00)	0.598 (1.00)	0.476 (1.00)
17q gain	62 (14%)	379	2e-05 (0.0136)	0.165 (1.00)	0.944 (1.00)	0.964 (1.00)	0.487 (1.00)	0.207 (1.00)	0.0433 (1.00)	0.338 (1.00)	0.0721 (1.00)	0.00671 (1.00)
19p gain	54 (12%)	387	7e-05 (0.0451)	0.931 (1.00)	0.497 (1.00)	0.0663 (1.00)	0.49 (1.00)	0.906 (1.00)	0.575 (1.00)	0.462 (1.00)	0.54 (1.00)	0.426 (1.00)
19q gain	78 (18%)	363	1e-05 (0.0079)	0.541 (1.00)	0.149 (1.00)	0.0431 (1.00)	0.0161 (1.00)	0.251 (1.00)	0.0163 (1.00)	0.057 (1.00)	0.00681 (1.00)	0.0872 (1.00)
xq gain	54 (12%)	387	1e-05 (0.0079)	0.00056 (0.333)	0.481 (1.00)	0.585 (1.00)	0.0394 (1.00)	0.00055 (0.328)	0.0815 (1.00)	0.104 (1.00)	0.427 (1.00)	0.0983 (1.00)
2p loss	26 (6%)	415	3e-05 (0.02)	0.00074 (0.434)	0.377 (1.00)	0.474 (1.00)	0.0124 (1.00)	0.294 (1.00)	0.0406 (1.00)	0.141 (1.00)	0.47 (1.00)	0.334 (1.00)
6p loss	52 (12%)	389	2e-05 (0.0136)	0.00177 (0.982)	0.15 (1.00)	0.912 (1.00)	0.0221 (1.00)	0.00848 (1.00)	0.092 (1.00)	0.016 (1.00)	0.0325 (1.00)	0.452 (1.00)
6q loss	70 (16%)	371	1e-05 (0.0079)	0.00118 (0.68)	0.9 (1.00)	0.814 (1.00)	0.0633 (1.00)	0.141 (1.00)	0.554 (1.00)	0.0603 (1.00)	0.109 (1.00)	0.447 (1.00)
7q loss	30 (7%)	411	1e-05 (0.0079)	0.0044 (1.00)	0.485 (1.00)	0.781 (1.00)	0.00579 (1.00)	0.281 (1.00)	0.00788 (1.00)	0.0504 (1.00)	0.0474 (1.00)	0.409 (1.00)
11p loss	62 (14%)	379	1e-05 (0.0079)	0.0152 (1.00)	0.0178 (1.00)	0.07 (1.00)	0.169 (1.00)	0.316 (1.00)	0.0522 (1.00)	0.0176 (1.00)	0.171 (1.00)	0.294 (1.00)
11q loss	61 (14%)	380	4e-05 (0.0263)	0.164 (1.00)	0.674 (1.00)	0.453 (1.00)	0.623 (1.00)	0.627 (1.00)	0.0648 (1.00)	0.37 (1.00)	0.169 (1.00)	0.227 (1.00)
18p loss	119 (27%)	322	1e-05 (0.0079)	0.367 (1.00)	0.773 (1.00)	0.658 (1.00)	0.558 (1.00)	0.249 (1.00)	0.0473 (1.00)	0.107 (1.00)	0.37 (1.00)	0.273 (1.00)
20p loss	22 (5%)	419	0.00262 (1.00)	0.00019 (0.118)	0.814 (1.00)	0.309 (1.00)	0.00049 (0.294)	0.0574 (1.00)	0.181 (1.00)	0.409 (1.00)	0.562 (1.00)	0.668 (1.00)
21q loss	180 (41%)	261	1e-05 (0.0079)	0.0135 (1.00)	0.101 (1.00)	0.294 (1.00)	0.0376 (1.00)	0.0016 (0.898)	0.00071 (0.417)	0.0043 (1.00)	0.00131 (0.751)	0.111 (1.00)
3p gain	53 (12%)	388	0.00196 (1.00)	0.0278 (1.00)	0.791 (1.00)	0.0247 (1.00)	0.624 (1.00)	0.226 (1.00)	0.188 (1.00)	0.588 (1.00)	0.373 (1.00)	0.0301 (1.00)
4p gain	21 (5%)	420	0.0788 (1.00)	0.324 (1.00)	0.912 (1.00)	0.271 (1.00)	0.208 (1.00)	0.321 (1.00)	0.515 (1.00)	0.162 (1.00)	0.35 (1.00)	0.235 (1.00)
4q gain	16 (4%)	425	0.435 (1.00)	0.222 (1.00)	0.691 (1.00)	0.0882 (1.00)	0.0207 (1.00)	0.429 (1.00)	0.494 (1.00)	0.0679 (1.00)	0.614 (1.00)	0.665 (1.00)
5q gain	44 (10%)	397	0.0111 (1.00)	0.248 (1.00)	0.853 (1.00)	0.275 (1.00)	0.196 (1.00)	0.366 (1.00)	0.417 (1.00)	0.64 (1.00)	0.148 (1.00)	0.806 (1.00)
8q gain	237 (54%)	204	0.00904 (1.00)	0.0164 (1.00)	0.676 (1.00)	0.298 (1.00)	0.0369 (1.00)	0.0171 (1.00)	0.0406 (1.00)	0.0374 (1.00)	0.619 (1.00)	0.372 (1.00)
9p gain	60 (14%)	381	0.0953 (1.00)	0.818 (1.00)	0.377 (1.00)	0.859 (1.00)	0.583 (1.00)	0.495 (1.00)	0.698 (1.00)	0.773 (1.00)	0.5 (1.00)	1 (1.00)
9q gain	78 (18%)	363	0.217 (1.00)	0.951 (1.00)	0.25 (1.00)	0.983 (1.00)	0.428 (1.00)	0.927 (1.00)	0.975 (1.00)	0.93 (1.00)	0.363 (1.00)	0.779 (1.00)
12q gain	77 (17%)	364	0.00363 (1.00)	0.953 (1.00)	0.439 (1.00)	0.425 (1.00)	0.966 (1.00)	0.278 (1.00)	0.157 (1.00)	0.388 (1.00)	0.231 (1.00)	0.109 (1.00)
16p gain	59 (13%)	382	0.00132 (0.755)	0.0075 (1.00)	0.395 (1.00)	0.113 (1.00)	0.0748 (1.00)	0.287 (1.00)	0.906 (1.00)	0.977 (1.00)	0.244 (1.00)	0.0952 (1.00)
16q gain	47 (11%)	394	0.00281 (1.00)	0.197 (1.00)	0.673 (1.00)	0.262 (1.00)	0.186 (1.00)	0.626 (1.00)	0.707 (1.00)	0.959 (1.00)	0.0505 (1.00)	0.0165 (1.00)
17p gain	29 (7%)	412	0.00097 (0.565)	0.404 (1.00)	0.665 (1.00)	0.684 (1.00)	0.191 (1.00)	0.216 (1.00)	0.0513 (1.00)	0.194 (1.00)	0.109 (1.00)	0.314 (1.00)
18q gain	54 (12%)	387	0.00666 (1.00)	0.00185 (1.00)	0.599 (1.00)	0.237 (1.00)	0.28 (1.00)	0.022 (1.00)	0.0155 (1.00)	0.0208 (1.00)	0.283 (1.00)	0.0378 (1.00)
22q gain	32 (7%)	409	0.0022 (1.00)	0.136 (1.00)	0.844 (1.00)	0.217 (1.00)	0.259 (1.00)	0.0666 (1.00)	0.234 (1.00)	0.622 (1.00)	0.0285 (1.00)	0.17 (1.00)
8q loss	33 (7%)	408	0.00086 (0.503)	0.808 (1.00)	0.826 (1.00)	0.372 (1.00)	0.754 (1.00)	0.985 (1.00)	0.0241 (1.00)	0.508 (1.00)	0.0309 (1.00)	0.227 (1.00)
13q loss	36 (8%)	405	0.00341 (1.00)	0.868 (1.00)	0.687 (1.00)	0.305 (1.00)	0.281 (1.00)	0.603 (1.00)	0.701 (1.00)	0.444 (1.00)	0.762 (1.00)	0.145 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1P GAIN MUTATED	27	5	4	12	3
1P GAIN WILD-TYPE	96	182	32	64	16

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S2. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1Q GAIN MUTATED	53	12	10	22	6
1Q GAIN WILD-TYPE	70	175	26	54	13

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S3. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
1Q GAIN MUTATED	10	7	9	9	30
1Q GAIN WILD-TYPE	55	55	37	28	32

Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S4. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
1Q GAIN MUTATED	23	23	17	40
1Q GAIN WILD-TYPE	56	152	62	67

Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S5. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2P GAIN MUTATED	35	8	12	16	6
2P GAIN WILD-TYPE	88	179	24	60	13

Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S6. Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
2P GAIN MUTATED	29	13	35
2P GAIN WILD-TYPE	157	120	86

Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S7. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2Q GAIN MUTATED	28	8	10	15	5
2Q GAIN WILD-TYPE	95	179	26	61	14

Figure S7. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S8. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3Q GAIN MUTATED	27	20	11	25	10
3Q GAIN WILD-TYPE	96	167	25	51	9

Figure S8. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S9. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5P GAIN MUTATED	59	16	7	17	3
5P GAIN WILD-TYPE	64	171	29	59	16

Figure S9. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S10. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
5P GAIN MUTATED	17	37	21
5P GAIN WILD-TYPE	109	59	93

Figure S10. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S11. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5P GAIN MUTATED	10	5	8	8	29
5P GAIN WILD-TYPE	55	57	38	29	33

Figure S11. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S12. Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
5P GAIN MUTATED	41	18	43
5P GAIN WILD-TYPE	145	115	78

Figure S12. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S13. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
5P GAIN MUTATED	14	32	10	46
5P GAIN WILD-TYPE	65	143	69	61

Figure S13. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S14. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6P GAIN MUTATED	53	6	1	14	4
6P GAIN WILD-TYPE	70	181	35	62	15

Figure S14. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S15. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
6P GAIN MUTATED	13	35	7
6P GAIN WILD-TYPE	113	61	107

Figure S15. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S16. Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
6P GAIN MUTATED	27	10	40
6P GAIN WILD-TYPE	159	123	81

Figure S16. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S17. Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
6P GAIN MUTATED	19	13	7	38
6P GAIN WILD-TYPE	60	162	72	69

Figure S17. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S18. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6Q GAIN MUTATED	45	5	0	11	3
6Q GAIN WILD-TYPE	78	182	36	65	16

Figure S18. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S19. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
6Q GAIN MUTATED	11	27	5
6Q GAIN WILD-TYPE	115	69	109

Figure S19. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.2

Table S20. Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
6Q GAIN MUTATED	5	4	5	5	21
6Q GAIN WILD-TYPE	60	58	41	32	41

Figure S20. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S21. Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
6Q GAIN MUTATED	24	8	31
6Q GAIN WILD-TYPE	162	125	90

Figure S21. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S22. Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
6Q GAIN MUTATED	17	11	6	29
6Q GAIN WILD-TYPE	62	164	73	78

Figure S22. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S23. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7P GAIN MUTATED	67	44	34	40	12
7P GAIN WILD-TYPE	56	143	2	36	7

Figure S23. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S24. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7Q GAIN MUTATED	53	43	34	30	9
7Q GAIN WILD-TYPE	70	144	2	46	10

Figure S24. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S25. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
8P GAIN MUTATED	44	82	16	23	17
8P GAIN WILD-TYPE	79	105	20	53	2

Figure S25. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S26. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10P GAIN MUTATED	39	9	14	35	1
10P GAIN WILD-TYPE	84	178	22	41	18

Figure S26. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.082

Table S27. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
10P GAIN MUTATED	22	37	18
10P GAIN WILD-TYPE	104	59	96

Figure S27. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S28. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10Q GAIN MUTATED	20	7	6	33	4
10Q GAIN WILD-TYPE	103	180	30	43	15

Figure S28. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S29. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11P GAIN MUTATED	35	10	3	13	3
11P GAIN WILD-TYPE	88	177	33	63	16

Figure S29. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S30. Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
11P GAIN MUTATED	23	8	32
11P GAIN WILD-TYPE	163	125	89

Figure S30. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S31. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11Q GAIN MUTATED	39	10	2	18	5
11Q GAIN WILD-TYPE	84	177	34	58	14

Figure S31. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S32. Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
11Q GAIN MUTATED	28	7	38
11Q GAIN WILD-TYPE	158	126	83

Figure S32. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.22

Table S33. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
11Q GAIN MUTATED	11	26	5	31
11Q GAIN WILD-TYPE	68	149	74	76

Figure S33. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.1

Table S34. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12P GAIN MUTATED	27	21	11	27	4
12P GAIN WILD-TYPE	96	166	25	49	15

Figure S34. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S35. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
13Q GAIN MUTATED	71	36	23	17	7
13Q GAIN WILD-TYPE	52	151	13	59	12

Figure S35. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.088

Table S36. Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
13Q GAIN MUTATED	36	50	30
13Q GAIN WILD-TYPE	90	46	84

Figure S36. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S37. Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
13Q GAIN MUTATED	3	5	16	16	24	19	6
13Q GAIN WILD-TYPE	35	16	33	46	17	21	15

Figure S37. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.076

Table S38. Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
13Q GAIN MUTATED	34	43	23	53
13Q GAIN WILD-TYPE	45	132	56	54

Figure S38. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S39. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
14Q GAIN MUTATED	19	5	4	1	0
14Q GAIN WILD-TYPE	104	182	32	75	19

Figure S39. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S40. Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
15Q GAIN MUTATED	16	5	3	15	0
15Q GAIN WILD-TYPE	107	182	33	61	19

Figure S40. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S41. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17Q GAIN MUTATED	30	10	6	12	4
17Q GAIN WILD-TYPE	93	177	30	64	15

Figure S41. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S42. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18P GAIN MUTATED	42	14	7	17	4
18P GAIN WILD-TYPE	81	173	29	59	15

Figure S42. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S43. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
18P GAIN MUTATED	16	36	13
18P GAIN WILD-TYPE	110	60	101

Figure S43. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.15

Table S44. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
18P GAIN MUTATED	27	18	39
18P GAIN WILD-TYPE	159	115	82

Figure S44. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S45. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
18P GAIN MUTATED	14	23	9	38
18P GAIN WILD-TYPE	65	152	70	69

Figure S45. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S46. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19P GAIN MUTATED	22	9	8	15	0
19P GAIN WILD-TYPE	101	178	28	61	19

Figure S46. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S47. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19Q GAIN MUTATED	36	13	9	20	0
19Q GAIN WILD-TYPE	87	174	27	56	19

Figure S47. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S48. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
20P GAIN MUTATED	93	58	25	52	15
20P GAIN WILD-TYPE	30	129	11	24	4

Figure S48. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S49. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
20P GAIN MUTATED	60	70	56
20P GAIN WILD-TYPE	66	26	58

Figure S49. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S50. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
20P GAIN MUTATED	16	19	17	28	29	32	2
20P GAIN WILD-TYPE	22	2	32	34	12	8	19

Figure S50. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S51. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
20P GAIN MUTATED	89	64	89
20P GAIN WILD-TYPE	97	69	32

Figure S51. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S52. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
20P GAIN MUTATED	39	84	36	83
20P GAIN WILD-TYPE	40	91	43	24

Figure S52. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S53. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
20P GAIN MUTATED	59	24	28	26	23	25
20P GAIN WILD-TYPE	17	34	32	32	13	33

Figure S53. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S54. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
20Q GAIN MUTATED	108	66	31	59	15
20Q GAIN WILD-TYPE	15	121	5	17	4

Figure S54. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S55. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
20Q GAIN MUTATED	64	84	65
20Q GAIN WILD-TYPE	62	12	49

Figure S55. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S56. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
20Q GAIN MUTATED	30	31	27	24	56
20Q GAIN WILD-TYPE	35	31	19	13	6

Figure S56. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S57. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
20Q GAIN MUTATED	22	19	19	38	31	37	2
20Q GAIN WILD-TYPE	16	2	30	24	10	3	19

Figure S57. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S58. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
20Q GAIN MUTATED	102	74	102
20Q GAIN WILD-TYPE	84	59	19

Figure S58. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S59. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
20Q GAIN MUTATED	41	100	40	97
20Q GAIN WILD-TYPE	38	75	39	10

Figure S59. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S60. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
20Q GAIN MUTATED	64	28	34	35	27	29
20Q GAIN WILD-TYPE	12	30	26	23	9	29

Figure S60. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.1

Table S61. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
21Q GAIN MUTATED	14	1	1	5	0
21Q GAIN WILD-TYPE	109	186	35	71	19

Figure S61. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.22

Table S62. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
21Q GAIN MUTATED	4	14	2
21Q GAIN WILD-TYPE	122	82	112

Figure S62. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S63. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
21Q GAIN MUTATED	5	3	0	13
21Q GAIN WILD-TYPE	74	172	79	94

Figure S63. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S64. Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
XQ GAIN MUTATED	26	8	11	4	5
XQ GAIN WILD-TYPE	97	179	25	72	14

Figure S64. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S65. Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1P LOSS MUTATED	38	2	3	15	1
1P LOSS WILD-TYPE	85	185	33	61	18

Figure S65. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S66. Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
1P LOSS MUTATED	12	27	5
1P LOSS WILD-TYPE	114	69	109

Figure S66. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S67. Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
1Q LOSS MUTATED	16	1	1	9	1
1Q LOSS WILD-TYPE	107	186	35	67	18

Figure S67. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S68. Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
1Q LOSS MUTATED	5	17	1
1Q LOSS WILD-TYPE	121	79	113

Figure S68. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S69. Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2P LOSS MUTATED	15	1	2	8	0
2P LOSS WILD-TYPE	108	186	34	68	19

Figure S69. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S70. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
2Q LOSS MUTATED	20	1	3	9	0
2Q LOSS WILD-TYPE	103	186	33	67	19

Figure S70. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S71. Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
2Q LOSS MUTATED	4	17	3
2Q LOSS WILD-TYPE	122	79	111

Figure S71. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S72. Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3P LOSS MUTATED	45	10	8	24	4
3P LOSS WILD-TYPE	78	177	28	52	15

Figure S72. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S73. Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
3P LOSS MUTATED	5	2	4	9	13	15	0
3P LOSS WILD-TYPE	33	19	45	53	28	25	21

Figure S73. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S74. Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
3Q LOSS MUTATED	32	3	7	11	1
3Q LOSS WILD-TYPE	91	184	29	65	18

Figure S74. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S75. Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
3Q LOSS MUTATED	2	3	0	6	17
3Q LOSS WILD-TYPE	63	59	46	31	45

Figure S75. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S76. Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
3Q LOSS MUTATED	3	0	1	1	10	13	0
3Q LOSS WILD-TYPE	35	21	48	61	31	27	21

Figure S76. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S77. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
4P LOSS MUTATED	76	27	12	47	5
4P LOSS WILD-TYPE	47	160	24	29	14

Figure S77. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S78. Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
4P LOSS MUTATED	34	53	38
4P LOSS WILD-TYPE	92	43	76

Figure S78. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S79. Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
4P LOSS MUTATED	11	2	18	17	17	25	3
4P LOSS WILD-TYPE	27	19	31	45	24	15	18

Figure S79. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S80. Gene #47: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
4P LOSS MUTATED	55	42	70
4P LOSS WILD-TYPE	131	91	51

Figure S80. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S81. Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
4P LOSS MUTATED	22	51	25	69
4P LOSS WILD-TYPE	57	124	54	38

Figure S81. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S82. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
4P LOSS MUTATED	46	19	15	17	13	22
4P LOSS WILD-TYPE	30	39	45	41	23	36

Figure S82. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S83. Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
4Q LOSS MUTATED	72	26	10	51	5
4Q LOSS WILD-TYPE	51	161	26	25	14

Figure S83. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S84. Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
4Q LOSS MUTATED	36	55	35
4Q LOSS WILD-TYPE	90	41	79

Figure S84. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S85. Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
4Q LOSS MUTATED	54	44	66
4Q LOSS WILD-TYPE	132	89	55

Figure S85. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S86. Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
4Q LOSS MUTATED	23	51	24	66
4Q LOSS WILD-TYPE	56	124	55	41

Figure S86. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S87. Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5P LOSS MUTATED	28	5	4	19	4
5P LOSS WILD-TYPE	95	182	32	57	15

Figure S87. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S88. Gene #49: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
5P LOSS MUTATED	17	13	30
5P LOSS WILD-TYPE	169	120	91

Figure S88. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S89. Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
5P LOSS MUTATED	10	15	6	29
5P LOSS WILD-TYPE	69	160	73	78

Figure S89. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S90. Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
5Q LOSS MUTATED	58	6	9	27	6
5Q LOSS WILD-TYPE	65	181	27	49	13

Figure S90. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S91. Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
5Q LOSS MUTATED	21	45	14
5Q LOSS WILD-TYPE	105	51	100

Figure S91. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S92. Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
5Q LOSS MUTATED	10	3	5	7	28
5Q LOSS WILD-TYPE	55	59	41	30	34

Figure S92. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S93. Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
5Q LOSS MUTATED	6	2	2	13	8	20	2
5Q LOSS WILD-TYPE	32	19	47	49	33	20	19

Figure S93. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S94. Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
5Q LOSS MUTATED	33	20	53
5Q LOSS WILD-TYPE	153	113	68

Figure S94. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S95. Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
5Q LOSS MUTATED	13	30	9	54
5Q LOSS WILD-TYPE	66	145	70	53

Figure S95. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S96. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
5Q LOSS MUTATED	39	12	11	10	9	10
5Q LOSS WILD-TYPE	37	46	49	48	27	48

Figure S96. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S97. Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6P LOSS MUTATED	17	7	5	20	3
6P LOSS WILD-TYPE	106	180	31	56	16

Figure S97. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S98. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
6Q LOSS MUTATED	22	11	8	25	4
6Q LOSS WILD-TYPE	101	176	28	51	15

Figure S98. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.24

Table S99. Gene #53: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7P LOSS MUTATED	12	1	1	6	0
7P LOSS WILD-TYPE	111	186	35	70	19

Figure S99. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S100. Gene #53: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
7P LOSS MUTATED	3	3	14
7P LOSS WILD-TYPE	183	130	107

Figure S100. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S101. Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
7Q LOSS MUTATED	16	1	0	12	1
7Q LOSS WILD-TYPE	107	186	36	64	18

Figure S101. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S102. Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
8P LOSS MUTATED	38	13	9	27	1
8P LOSS WILD-TYPE	85	174	27	49	18

Figure S102. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S103. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
8P LOSS MUTATED	53	2	16
8P LOSS WILD-TYPE	148	71	56

Figure S103. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S104. Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
9P LOSS MUTATED	58	14	16	53	9
9P LOSS WILD-TYPE	65	173	20	23	10

Figure S104. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S105. Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
9P LOSS MUTATED	27	54	29
9P LOSS WILD-TYPE	99	42	85

Figure S105. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.18

Table S106. Gene #57: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
9P LOSS MUTATED	6	38	8	30
9P LOSS WILD-TYPE	28	45	47	61

Figure S106. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S107. Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
9P LOSS MUTATED	7	12	19	9	36
9P LOSS WILD-TYPE	58	50	27	28	26

Figure S107. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S108. Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
9P LOSS MUTATED	12	1	10	24	13	21	2
9P LOSS WILD-TYPE	26	20	39	38	28	19	19

Figure S108. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S109. Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
9P LOSS MUTATED	48	38	63
9P LOSS WILD-TYPE	138	95	58

Figure S109. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S110. Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
9P LOSS MUTATED	21	49	19	60
9P LOSS WILD-TYPE	58	126	60	47

Figure S110. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S111. Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
9Q LOSS MUTATED	41	12	11	35	5
9Q LOSS WILD-TYPE	82	175	25	41	14

Figure S111. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S112. Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
9Q LOSS MUTATED	18	36	23
9Q LOSS WILD-TYPE	108	60	91

Figure S112. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S113. Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
9Q LOSS MUTATED	7	10	14	4	28
9Q LOSS WILD-TYPE	58	52	32	33	34

Figure S113. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S114. Gene #58: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
9Q LOSS MUTATED	31	24	49
9Q LOSS WILD-TYPE	155	109	72

Figure S114. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S115. Gene #58: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
9Q LOSS MUTATED	13	33	12	46
9Q LOSS WILD-TYPE	66	142	67	61

Figure S115. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S116. Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10P LOSS MUTATED	34	8	3	12	7
10P LOSS WILD-TYPE	89	179	33	64	12

Figure S116. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S117. Gene #59: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
10P LOSS MUTATED	24	8	32
10P LOSS WILD-TYPE	162	125	89

Figure S117. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.2

Table S118. Gene #59: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
10P LOSS MUTATED	12	25	2	25
10P LOSS WILD-TYPE	67	150	77	82

Figure S118. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S119. Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
10Q LOSS MUTATED	42	6	7	7	5
10Q LOSS WILD-TYPE	81	181	29	69	14

Figure S119. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.19

Table S120. Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
10Q LOSS MUTATED	12	26	10
10Q LOSS WILD-TYPE	114	70	104

Figure S120. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S121. Gene #60: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
10Q LOSS MUTATED	27	8	32
10Q LOSS WILD-TYPE	159	125	89

Figure S121. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.1

Table S122. Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
10Q LOSS MUTATED	14	18	5	30
10Q LOSS WILD-TYPE	65	157	74	77

Figure S122. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S123. Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11P LOSS MUTATED	33	7	6	16	0
11P LOSS WILD-TYPE	90	180	30	60	19

Figure S123. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S124. Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
11Q LOSS MUTATED	28	10	6	15	2
11Q LOSS WILD-TYPE	95	177	30	61	17

Figure S124. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S125. Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12P LOSS MUTATED	41	2	5	13	2
12P LOSS WILD-TYPE	82	185	31	63	17

Figure S125. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S126. Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
12P LOSS MUTATED	2	32	6
12P LOSS WILD-TYPE	124	64	108

Figure S126. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S127. Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
12P LOSS MUTATED	3	3	6	3	20
12P LOSS WILD-TYPE	62	59	40	34	42

Figure S127. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S128. Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
12P LOSS MUTATED	2	0	2	10	4	17	0
12P LOSS WILD-TYPE	36	21	47	52	37	23	21

Figure S128. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.051

Table S129. Gene #63: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
12P LOSS MUTATED	20	11	32
12P LOSS WILD-TYPE	166	122	89

Figure S129. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S130. Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
12P LOSS MUTATED	6	19	6	32
12P LOSS WILD-TYPE	73	156	73	75

Figure S130. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S131. Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
12Q LOSS MUTATED	34	1	3	12	2
12Q LOSS WILD-TYPE	89	186	33	64	17

Figure S131. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S132. Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
12Q LOSS MUTATED	3	25	5
12Q LOSS WILD-TYPE	123	71	109

Figure S132. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S133. Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
14Q LOSS MUTATED	47	17	5	37	5
14Q LOSS WILD-TYPE	76	170	31	39	14

Figure S133. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S134. Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
14Q LOSS MUTATED	22	41	21
14Q LOSS WILD-TYPE	104	55	93

Figure S134. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S135. Gene #66: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
14Q LOSS MUTATED	37	24	50
14Q LOSS WILD-TYPE	149	109	71

Figure S135. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.057

Table S136. Gene #66: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
14Q LOSS MUTATED	14	36	15	46
14Q LOSS WILD-TYPE	65	139	64	61

Figure S136. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S137. Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
15Q LOSS MUTATED	43	13	9	22	3
15Q LOSS WILD-TYPE	80	174	27	54	16

Figure S137. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.076

Table S138. Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
15Q LOSS MUTATED	8	4	9	4	23
15Q LOSS WILD-TYPE	57	58	37	33	39

Figure S138. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S139. Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
16P LOSS MUTATED	55	10	4	29	2
16P LOSS WILD-TYPE	68	177	32	47	17

Figure S139. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S140. Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
16P LOSS MUTATED	19	36	17
16P LOSS WILD-TYPE	107	60	97

Figure S140. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S141. Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
16P LOSS MUTATED	7	5	5	4	32
16P LOSS WILD-TYPE	58	57	41	33	30

Figure S141. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S142. Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
16P LOSS MUTATED	7	0	4	9	8	22	3
16P LOSS WILD-TYPE	31	21	45	53	33	18	18

Figure S142. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S143. Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
16P LOSS MUTATED	31	17	52
16P LOSS WILD-TYPE	155	116	69

Figure S143. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S144. Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
16P LOSS MUTATED	12	32	10	46
16P LOSS WILD-TYPE	67	143	69	61

Figure S144. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S145. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
16P LOSS MUTATED	33	12	6	8	15	6
16P LOSS WILD-TYPE	43	46	54	50	21	52

Figure S145. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S146. Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
16Q LOSS MUTATED	60	16	3	32	4
16Q LOSS WILD-TYPE	63	171	33	44	15

Figure S146. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S147. Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
16Q LOSS MUTATED	16	41	25
16Q LOSS WILD-TYPE	110	55	89

Figure S147. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S148. Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
16Q LOSS MUTATED	6	10	10	5	33
16Q LOSS WILD-TYPE	59	52	36	32	29

Figure S148. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S149. Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
16Q LOSS MUTATED	8	0	8	14	8	24	2
16Q LOSS WILD-TYPE	30	21	41	48	33	16	19

Figure S149. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S150. Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
16Q LOSS MUTATED	36	24	55
16Q LOSS WILD-TYPE	150	109	66

Figure S150. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S151. Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
16Q LOSS MUTATED	14	37	14	50
16Q LOSS WILD-TYPE	65	138	65	57

Figure S151. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.063

Table S152. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
16Q LOSS MUTATED	36	12	10	9	13	12
16Q LOSS WILD-TYPE	40	46	50	49	23	46

Figure S152. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S153. Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17P LOSS MUTATED	76	17	16	48	7
17P LOSS WILD-TYPE	47	170	20	28	12

Figure S153. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S154. Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
17P LOSS MUTATED	36	62	23
17P LOSS WILD-TYPE	90	34	91

Figure S154. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S155. Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
17P LOSS MUTATED	14	10	18	12	35
17P LOSS WILD-TYPE	51	52	28	25	27

Figure S155. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S156. Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
17P LOSS MUTATED	14	2	7	22	17	25	2
17P LOSS WILD-TYPE	24	19	42	40	24	15	19

Figure S156. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S157. Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
17P LOSS MUTATED	67	30	66
17P LOSS WILD-TYPE	119	103	55

Figure S157. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S158. Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
17P LOSS MUTATED	26	62	16	59
17P LOSS WILD-TYPE	53	113	63	48

Figure S158. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S159. Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
17Q LOSS MUTATED	39	8	5	18	4
17Q LOSS WILD-TYPE	84	179	31	58	15

Figure S159. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S160. Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
17Q LOSS MUTATED	13	31	10
17Q LOSS WILD-TYPE	113	65	104

Figure S160. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S161. Gene #71: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
17Q LOSS MUTATED	12	21	7	33
17Q LOSS WILD-TYPE	67	154	72	74

Figure S161. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S162. Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18P LOSS MUTATED	42	28	13	33	3
18P LOSS WILD-TYPE	81	159	23	43	16

Figure S162. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S163. Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
18Q LOSS MUTATED	66	30	17	38	3
18Q LOSS WILD-TYPE	57	157	19	38	16

Figure S163. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.082

Table S164. Gene #73: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
18Q LOSS MUTATED	59	34	61
18Q LOSS WILD-TYPE	127	99	60

Figure S164. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S165. Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19P LOSS MUTATED	66	4	8	30	7
19P LOSS WILD-TYPE	57	183	28	46	12

Figure S165. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S166. Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
19P LOSS MUTATED	21	53	13
19P LOSS WILD-TYPE	105	43	101

Figure S166. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S167. Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19P LOSS MUTATED	8	3	8	4	32
19P LOSS WILD-TYPE	57	59	38	33	30

Figure S167. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S168. Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
19P LOSS MUTATED	5	2	3	14	9	22	0
19P LOSS WILD-TYPE	33	19	46	48	32	18	21

Figure S168. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S169. Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
19P LOSS MUTATED	35	16	63
19P LOSS WILD-TYPE	151	117	58

Figure S169. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S170. Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
19P LOSS MUTATED	12	31	9	62
19P LOSS WILD-TYPE	67	144	70	45

Figure S170. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S171. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
19P LOSS MUTATED	37	14	12	12	8	7
19P LOSS WILD-TYPE	39	44	48	46	28	51

Figure S171. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S172. Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
19Q LOSS MUTATED	51	4	7	18	7
19Q LOSS WILD-TYPE	72	183	29	58	12

Figure S172. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S173. Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
19Q LOSS MUTATED	15	40	9
19Q LOSS WILD-TYPE	111	56	105

Figure S173. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S174. Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
19Q LOSS MUTATED	5	2	8	5	23
19Q LOSS WILD-TYPE	60	60	38	32	39

Figure S174. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S175. Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
19Q LOSS MUTATED	3	1	2	13	8	16	0
19Q LOSS WILD-TYPE	35	20	47	49	33	24	21

Figure S175. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S176. Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
19Q LOSS MUTATED	28	10	49
19Q LOSS WILD-TYPE	158	123	72

Figure S176. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S177. Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
19Q LOSS MUTATED	11	20	7	49
19Q LOSS WILD-TYPE	68	155	72	58

Figure S177. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.16

Table S178. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
19Q LOSS MUTATED	28	12	12	6	5	4
19Q LOSS WILD-TYPE	48	46	48	52	31	54

Figure S178. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S179. Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
20P LOSS MUTATED	1	12	3
20P LOSS WILD-TYPE	125	84	111

Figure S179. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S180. Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
21Q LOSS MUTATED	68	35	16	50	11
21Q LOSS WILD-TYPE	55	152	20	26	8

Figure S180. Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S181. Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
22Q LOSS MUTATED	67	17	11	43	8
22Q LOSS WILD-TYPE	56	170	25	33	11

Figure S181. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S182. Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
22Q LOSS MUTATED	31	52	27
22Q LOSS WILD-TYPE	95	44	87

Figure S182. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S183. Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
22Q LOSS MUTATED	48	34	63
22Q LOSS WILD-TYPE	138	99	58

Figure S183. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S184. Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
22Q LOSS MUTATED	20	47	18	60
22Q LOSS WILD-TYPE	59	128	61	47

Figure S184. Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0079

Table S185. Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
XQ LOSS MUTATED	23	4	3	20	1
XQ LOSS WILD-TYPE	100	183	33	56	18

Figure S185. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.033

Table S186. Gene #79: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	96	114
XQ LOSS MUTATED	14	20	2
XQ LOSS WILD-TYPE	112	76	112

Figure S186. Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly arm-level cnvs = 79
Number of molecular subtypes = 10
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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