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

Bladder Urothelial Carcinoma (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/C19K492V

Overview

Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 408 patients, 68 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 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, 68 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
9q loss	169 (41%)	239	1e-05 (0.008)	4e-05 (0.0302)	0.0282 (1.00)	0.0104 (1.00)	0.00046 (0.335)	1e-05 (0.008)	0.027 (1.00)	0.00068 (0.492)	1e-05 (0.008)	1e-05 (0.008)
3p loss	52 (13%)	356	0.301 (1.00)	0.125 (1.00)	0.0217 (1.00)	0.0248 (1.00)	1e-05 (0.008)	1e-05 (0.008)	0.442 (1.00)	0.00092 (0.661)	3e-05 (0.0227)	0.00015 (0.112)
11p loss	180 (44%)	228	1e-05 (0.008)	1e-05 (0.008)	0.181 (1.00)	0.799 (1.00)	0.00011 (0.0821)	0.00038 (0.277)	0.132 (1.00)	0.0879 (1.00)	0.00023 (0.171)	0.00069 (0.497)
15q loss	144 (35%)	264	1e-05 (0.008)	0.00033 (0.242)	0.106 (1.00)	0.315 (1.00)	0.342 (1.00)	0.0167 (1.00)	0.0153 (1.00)	1e-05 (0.008)	0.0125 (1.00)	0.00013 (0.0968)
9p gain	68 (17%)	340	1e-05 (0.008)	0.13 (1.00)	0.858 (1.00)	0.585 (1.00)	0.447 (1.00)	0.41 (1.00)	0.379 (1.00)	0.245 (1.00)	6e-05 (0.0449)	1e-05 (0.008)
9p loss	174 (43%)	234	1e-05 (0.008)	0.00175 (1.00)	0.289 (1.00)	0.0898 (1.00)	0.0628 (1.00)	0.00329 (1.00)	0.0422 (1.00)	0.00136 (0.962)	2e-05 (0.0152)	1e-05 (0.008)
2p gain	110 (27%)	298	1e-05 (0.008)	0.00029 (0.214)	0.326 (1.00)	0.735 (1.00)	0.196 (1.00)	0.0337 (1.00)	0.0968 (1.00)	0.0141 (1.00)	0.232 (1.00)	0.00196 (1.00)
3q gain	178 (44%)	230	4e-05 (0.0302)	0.951 (1.00)	0.453 (1.00)	0.994 (1.00)	0.215 (1.00)	0.0636 (1.00)	0.00898 (1.00)	0.00942 (1.00)	0.00641 (1.00)	1e-05 (0.008)
7p gain	172 (42%)	236	1e-05 (0.008)	0.0129 (1.00)	0.0135 (1.00)	0.338 (1.00)	0.63 (1.00)	0.121 (1.00)	0.295 (1.00)	0.0346 (1.00)	0.246 (1.00)	0.00025 (0.185)
9q gain	56 (14%)	352	5e-05 (0.0375)	0.0277 (1.00)	0.88 (1.00)	0.0295 (1.00)	0.0389 (1.00)	0.00259 (1.00)	0.849 (1.00)	0.311 (1.00)	0.00049 (0.356)	3e-05 (0.0227)
18p gain	116 (28%)	292	1e-05 (0.008)	0.00053 (0.385)	0.951 (1.00)	0.911 (1.00)	0.201 (1.00)	0.0592 (1.00)	0.39 (1.00)	0.127 (1.00)	0.0585 (1.00)	5e-05 (0.0375)
6p loss	100 (25%)	308	1e-05 (0.008)	0.00027 (0.199)	0.637 (1.00)	0.758 (1.00)	0.121 (1.00)	0.00544 (1.00)	0.242 (1.00)	0.0108 (1.00)	0.224 (1.00)	0.00096 (0.687)
6q loss	156 (38%)	252	1e-05 (0.008)	0.00387 (1.00)	0.832 (1.00)	0.488 (1.00)	0.395 (1.00)	0.0894 (1.00)	0.179 (1.00)	0.00456 (1.00)	0.598 (1.00)	5e-05 (0.0375)
10q loss	127 (31%)	281	1e-05 (0.008)	0.00023 (0.171)	0.513 (1.00)	0.581 (1.00)	0.0177 (1.00)	0.156 (1.00)	0.183 (1.00)	0.0589 (1.00)	0.253 (1.00)	0.0321 (1.00)
13q loss	85 (21%)	323	0.0003 (0.221)	0.161 (1.00)	0.0104 (1.00)	0.103 (1.00)	0.0393 (1.00)	0.162 (1.00)	0.24 (1.00)	1e-05 (0.008)	0.0131 (1.00)	0.0014 (0.988)
14q loss	119 (29%)	289	1e-05 (0.008)	0.649 (1.00)	0.0679 (1.00)	0.0375 (1.00)	0.0908 (1.00)	0.00037 (0.27)	0.00167 (1.00)	0.031 (1.00)	0.00753 (1.00)	6e-05 (0.0449)
22q loss	159 (39%)	249	1e-05 (0.008)	0.00516 (1.00)	0.636 (1.00)	0.0165 (1.00)	0.0127 (1.00)	0.0211 (1.00)	0.153 (1.00)	0.00332 (1.00)	0.0716 (1.00)	3e-05 (0.0227)
1p gain	89 (22%)	319	4e-05 (0.0302)	0.027 (1.00)	0.292 (1.00)	0.223 (1.00)	0.444 (1.00)	0.734 (1.00)	0.788 (1.00)	0.249 (1.00)	0.794 (1.00)	0.0485 (1.00)
2q gain	55 (13%)	353	1e-05 (0.008)	0.135 (1.00)	0.616 (1.00)	0.297 (1.00)	0.732 (1.00)	0.71 (1.00)	0.101 (1.00)	0.36 (1.00)	0.682 (1.00)	0.426 (1.00)
3p gain	140 (34%)	268	0.00048 (0.349)	0.781 (1.00)	0.158 (1.00)	0.234 (1.00)	0.00875 (1.00)	0.0137 (1.00)	0.0132 (1.00)	0.0412 (1.00)	0.00975 (1.00)	0.0003 (0.221)
5p gain	166 (41%)	242	1e-05 (0.008)	0.39 (1.00)	0.0427 (1.00)	0.24 (1.00)	0.167 (1.00)	0.00143 (1.00)	0.837 (1.00)	0.00253 (1.00)	0.0915 (1.00)	0.00459 (1.00)
7q gain	150 (37%)	258	1e-05 (0.008)	0.00682 (1.00)	0.163 (1.00)	0.83 (1.00)	0.501 (1.00)	0.135 (1.00)	0.108 (1.00)	0.118 (1.00)	0.848 (1.00)	0.00456 (1.00)
10p gain	117 (29%)	291	1e-05 (0.008)	0.787 (1.00)	0.817 (1.00)	0.468 (1.00)	0.605 (1.00)	0.0253 (1.00)	0.93 (1.00)	0.753 (1.00)	0.765 (1.00)	0.00931 (1.00)
10q gain	44 (11%)	364	0.00022 (0.163)	0.195 (1.00)	0.362 (1.00)	0.371 (1.00)	0.474 (1.00)	0.0255 (1.00)	0.419 (1.00)	0.994 (1.00)	0.137 (1.00)	0.0735 (1.00)
12p gain	115 (28%)	293	3e-05 (0.0227)	0.0461 (1.00)	0.705 (1.00)	0.404 (1.00)	0.855 (1.00)	0.872 (1.00)	0.899 (1.00)	0.0249 (1.00)	0.338 (1.00)	0.127 (1.00)
19p gain	88 (22%)	320	0.00033 (0.242)	0.62 (1.00)	0.507 (1.00)	0.597 (1.00)	0.137 (1.00)	0.38 (1.00)	0.609 (1.00)	0.473 (1.00)	0.127 (1.00)	0.738 (1.00)
19q gain	135 (33%)	273	1e-05 (0.008)	0.313 (1.00)	0.443 (1.00)	0.679 (1.00)	0.53 (1.00)	0.433 (1.00)	0.5 (1.00)	0.0397 (1.00)	0.152 (1.00)	0.195 (1.00)
20p gain	202 (50%)	206	2e-05 (0.0152)	0.024 (1.00)	0.569 (1.00)	0.0486 (1.00)	0.287 (1.00)	0.022 (1.00)	0.314 (1.00)	0.0707 (1.00)	0.0268 (1.00)	0.0608 (1.00)
20q gain	230 (56%)	178	1e-05 (0.008)	0.0639 (1.00)	0.372 (1.00)	0.18 (1.00)	0.461 (1.00)	0.211 (1.00)	0.2 (1.00)	0.128 (1.00)	0.219 (1.00)	0.0153 (1.00)
21q gain	117 (29%)	291	1e-05 (0.008)	0.00936 (1.00)	0.5 (1.00)	0.266 (1.00)	0.00381 (1.00)	0.00433 (1.00)	0.00264 (1.00)	0.00439 (1.00)	0.0204 (1.00)	0.173 (1.00)
2q loss	90 (22%)	318	0.00026 (0.192)	0.00099 (0.707)	0.752 (1.00)	0.543 (1.00)	0.0506 (1.00)	0.0553 (1.00)	0.733 (1.00)	0.694 (1.00)	0.0356 (1.00)	0.0119 (1.00)
4p loss	142 (35%)	266	1e-05 (0.008)	0.00934 (1.00)	0.386 (1.00)	0.445 (1.00)	0.0207 (1.00)	0.00162 (1.00)	0.0781 (1.00)	0.0285 (1.00)	0.0308 (1.00)	0.101 (1.00)
4q loss	136 (33%)	272	1e-05 (0.008)	0.00226 (1.00)	0.139 (1.00)	0.192 (1.00)	0.163 (1.00)	0.00461 (1.00)	0.592 (1.00)	0.0523 (1.00)	0.00384 (1.00)	0.00314 (1.00)
5q loss	159 (39%)	249	1e-05 (0.008)	0.0107 (1.00)	0.795 (1.00)	0.188 (1.00)	0.334 (1.00)	0.0599 (1.00)	0.227 (1.00)	0.019 (1.00)	0.288 (1.00)	0.0135 (1.00)
8p loss	185 (45%)	223	1e-05 (0.008)	0.0189 (1.00)	0.146 (1.00)	0.102 (1.00)	0.0258 (1.00)	0.15 (1.00)	0.167 (1.00)	0.151 (1.00)	0.285 (1.00)	0.00379 (1.00)
11q loss	131 (32%)	277	1e-05 (0.008)	0.00096 (0.687)	0.0419 (1.00)	0.156 (1.00)	0.0412 (1.00)	0.194 (1.00)	0.594 (1.00)	0.493 (1.00)	0.528 (1.00)	0.228 (1.00)
12q loss	57 (14%)	351	2e-05 (0.0152)	0.435 (1.00)	0.367 (1.00)	0.407 (1.00)	0.813 (1.00)	0.664 (1.00)	1 (1.00)	0.653 (1.00)	0.828 (1.00)	0.0689 (1.00)
16p loss	106 (26%)	302	1e-05 (0.008)	0.0242 (1.00)	0.658 (1.00)	0.604 (1.00)	0.848 (1.00)	0.605 (1.00)	0.313 (1.00)	0.117 (1.00)	0.0663 (1.00)	0.0106 (1.00)
16q loss	104 (25%)	304	1e-05 (0.008)	0.0201 (1.00)	0.589 (1.00)	0.903 (1.00)	0.495 (1.00)	0.885 (1.00)	0.915 (1.00)	0.0689 (1.00)	0.773 (1.00)	0.00756 (1.00)
17p loss	182 (45%)	226	1e-05 (0.008)	0.641 (1.00)	0.911 (1.00)	0.53 (1.00)	0.446 (1.00)	0.00942 (1.00)	0.676 (1.00)	0.0154 (1.00)	0.163 (1.00)	0.00347 (1.00)
1q gain	128 (31%)	280	0.00155 (1.00)	0.329 (1.00)	0.675 (1.00)	0.973 (1.00)	0.452 (1.00)	0.829 (1.00)	0.332 (1.00)	0.532 (1.00)	0.306 (1.00)	0.47 (1.00)
4p gain	39 (10%)	369	0.0602 (1.00)	0.00389 (1.00)	0.606 (1.00)	0.416 (1.00)	0.0183 (1.00)	0.00716 (1.00)	0.01 (1.00)	0.547 (1.00)	0.323 (1.00)	0.57 (1.00)
4q gain	25 (6%)	383	0.0386 (1.00)	0.215 (1.00)	0.546 (1.00)	0.204 (1.00)	0.0799 (1.00)	0.321 (1.00)	0.0328 (1.00)	0.466 (1.00)	0.319 (1.00)	0.27 (1.00)
5q gain	51 (12%)	357	0.0173 (1.00)	0.694 (1.00)	0.00997 (1.00)	0.136 (1.00)	0.383 (1.00)	0.362 (1.00)	0.486 (1.00)	0.187 (1.00)	0.621 (1.00)	0.0686 (1.00)
6p gain	75 (18%)	333	0.00365 (1.00)	0.413 (1.00)	0.848 (1.00)	0.133 (1.00)	0.575 (1.00)	0.172 (1.00)	0.944 (1.00)	0.665 (1.00)	0.222 (1.00)	0.297 (1.00)
6q gain	41 (10%)	367	0.0442 (1.00)	0.329 (1.00)	0.975 (1.00)	0.0405 (1.00)	0.599 (1.00)	0.181 (1.00)	0.503 (1.00)	0.445 (1.00)	0.0412 (1.00)	0.0254 (1.00)
8p gain	92 (23%)	316	0.00064 (0.463)	0.273 (1.00)	0.15 (1.00)	0.037 (1.00)	0.286 (1.00)	0.806 (1.00)	0.22 (1.00)	0.0196 (1.00)	0.701 (1.00)	0.107 (1.00)
8q gain	204 (50%)	204	0.00087 (0.626)	0.125 (1.00)	0.0556 (1.00)	0.138 (1.00)	0.807 (1.00)	0.98 (1.00)	0.357 (1.00)	0.0328 (1.00)	0.737 (1.00)	0.0582 (1.00)
11p gain	29 (7%)	379	0.00412 (1.00)	0.115 (1.00)	0.195 (1.00)	0.153 (1.00)	0.214 (1.00)	0.0537 (1.00)	0.968 (1.00)	0.469 (1.00)	0.00401 (1.00)	0.0333 (1.00)
11q gain	48 (12%)	360	0.00638 (1.00)	0.534 (1.00)	0.199 (1.00)	0.0316 (1.00)	0.646 (1.00)	0.00295 (1.00)	0.814 (1.00)	0.751 (1.00)	0.0158 (1.00)	0.121 (1.00)
12q gain	90 (22%)	318	0.00228 (1.00)	0.554 (1.00)	0.0682 (1.00)	0.0129 (1.00)	0.152 (1.00)	0.249 (1.00)	0.593 (1.00)	0.057 (1.00)	0.8 (1.00)	0.0376 (1.00)
13q gain	100 (25%)	308	0.00966 (1.00)	0.835 (1.00)	0.942 (1.00)	0.748 (1.00)	0.381 (1.00)	0.593 (1.00)	0.722 (1.00)	0.825 (1.00)	0.232 (1.00)	0.0162 (1.00)
14q gain	59 (14%)	349	0.00057 (0.413)	0.355 (1.00)	0.379 (1.00)	0.15 (1.00)	0.0512 (1.00)	0.0906 (1.00)	0.743 (1.00)	0.213 (1.00)	0.569 (1.00)	0.453 (1.00)
15q gain	34 (8%)	374	0.285 (1.00)	0.0022 (1.00)	0.709 (1.00)	0.576 (1.00)	0.775 (1.00)	0.0215 (1.00)	0.1 (1.00)	0.73 (1.00)	0.209 (1.00)	0.146 (1.00)
16p gain	75 (18%)	333	0.0416 (1.00)	0.303 (1.00)	0.43 (1.00)	0.274 (1.00)	0.31 (1.00)	0.0796 (1.00)	0.448 (1.00)	0.264 (1.00)	0.539 (1.00)	0.453 (1.00)
16q gain	81 (20%)	327	0.114 (1.00)	0.0985 (1.00)	0.327 (1.00)	0.196 (1.00)	0.26 (1.00)	0.0879 (1.00)	0.228 (1.00)	0.137 (1.00)	0.639 (1.00)	0.204 (1.00)
17p gain	56 (14%)	352	0.00036 (0.264)	0.165 (1.00)	0.427 (1.00)	0.96 (1.00)	0.482 (1.00)	0.0348 (1.00)	0.0261 (1.00)	0.195 (1.00)	0.113 (1.00)	0.027 (1.00)
17q gain	136 (33%)	272	0.00079 (0.569)	0.0745 (1.00)	0.508 (1.00)	0.541 (1.00)	0.109 (1.00)	0.273 (1.00)	0.17 (1.00)	0.175 (1.00)	0.164 (1.00)	0.00133 (0.943)
18q gain	63 (15%)	345	0.00118 (0.841)	0.0119 (1.00)	0.323 (1.00)	0.302 (1.00)	0.597 (1.00)	0.99 (1.00)	0.0872 (1.00)	0.549 (1.00)	0.299 (1.00)	0.00595 (1.00)
22q gain	50 (12%)	358	0.00129 (0.916)	0.00146 (1.00)	0.591 (1.00)	0.567 (1.00)	0.00128 (0.91)	0.0664 (1.00)	0.139 (1.00)	0.329 (1.00)	0.0526 (1.00)	0.104 (1.00)
xq gain	49 (12%)	359	0.0193 (1.00)	0.0814 (1.00)	0.749 (1.00)	0.78 (1.00)	0.491 (1.00)	0.348 (1.00)	0.148 (1.00)	0.225 (1.00)	0.251 (1.00)	0.568 (1.00)
1p loss	30 (7%)	378	0.115 (1.00)	0.521 (1.00)	0.252 (1.00)	0.122 (1.00)	0.62 (1.00)	0.388 (1.00)	0.417 (1.00)	0.834 (1.00)	0.784 (1.00)	0.785 (1.00)
1q loss	30 (7%)	378	0.0303 (1.00)	0.846 (1.00)	0.4 (1.00)	0.957 (1.00)	0.534 (1.00)	0.602 (1.00)	0.857 (1.00)	0.257 (1.00)	0.52 (1.00)	0.0501 (1.00)
2p loss	44 (11%)	364	0.0881 (1.00)	0.161 (1.00)	0.961 (1.00)	0.749 (1.00)	0.22 (1.00)	0.0891 (1.00)	0.49 (1.00)	0.698 (1.00)	0.183 (1.00)	0.161 (1.00)
3q loss	23 (6%)	385	0.599 (1.00)	0.44 (1.00)	0.00328 (1.00)	0.0134 (1.00)	0.058 (1.00)	0.0139 (1.00)	0.89 (1.00)	0.233 (1.00)	0.00094 (0.674)	0.142 (1.00)
5p loss	54 (13%)	354	0.0358 (1.00)	0.444 (1.00)	0.316 (1.00)	0.665 (1.00)	0.514 (1.00)	0.017 (1.00)	0.896 (1.00)	0.702 (1.00)	0.0595 (1.00)	0.0265 (1.00)
7p loss	19 (5%)	389	0.305 (1.00)	0.629 (1.00)	0.268 (1.00)	0.62 (1.00)	0.803 (1.00)	0.776 (1.00)	0.244 (1.00)	0.0988 (1.00)	0.263 (1.00)	0.239 (1.00)
7q loss	27 (7%)	381	0.0334 (1.00)	0.838 (1.00)	0.323 (1.00)	0.428 (1.00)	0.683 (1.00)	0.989 (1.00)	0.44 (1.00)	0.232 (1.00)	0.562 (1.00)	0.296 (1.00)
8q loss	33 (8%)	375	0.0991 (1.00)	0.815 (1.00)	0.32 (1.00)	0.0096 (1.00)	0.0879 (1.00)	0.187 (1.00)	0.287 (1.00)	0.649 (1.00)	0.647 (1.00)	0.669 (1.00)
10p loss	73 (18%)	335	0.0376 (1.00)	0.0148 (1.00)	0.911 (1.00)	0.266 (1.00)	0.00474 (1.00)	0.00412 (1.00)	0.544 (1.00)	0.125 (1.00)	0.415 (1.00)	0.348 (1.00)
12p loss	53 (13%)	355	0.00745 (1.00)	0.621 (1.00)	0.944 (1.00)	0.474 (1.00)	0.086 (1.00)	0.117 (1.00)	0.523 (1.00)	0.44 (1.00)	0.143 (1.00)	0.269 (1.00)
17q loss	42 (10%)	366	0.00134 (0.949)	0.705 (1.00)	0.814 (1.00)	0.697 (1.00)	0.569 (1.00)	0.745 (1.00)	0.794 (1.00)	0.774 (1.00)	0.837 (1.00)	0.582 (1.00)
18p loss	98 (24%)	310	0.00068 (0.492)	0.466 (1.00)	0.45 (1.00)	0.365 (1.00)	0.596 (1.00)	0.266 (1.00)	0.171 (1.00)	0.835 (1.00)	0.114 (1.00)	0.256 (1.00)
18q loss	144 (35%)	264	0.0052 (1.00)	0.412 (1.00)	0.683 (1.00)	0.744 (1.00)	0.638 (1.00)	0.777 (1.00)	0.00185 (1.00)	0.00217 (1.00)	0.0833 (1.00)	0.334 (1.00)
19p loss	94 (23%)	314	0.00127 (0.904)	0.529 (1.00)	0.641 (1.00)	0.49 (1.00)	0.0922 (1.00)	0.0286 (1.00)	0.256 (1.00)	0.306 (1.00)	0.339 (1.00)	0.0686 (1.00)
19q loss	57 (14%)	351	0.0166 (1.00)	1 (1.00)	0.204 (1.00)	0.0935 (1.00)	0.399 (1.00)	0.294 (1.00)	0.0704 (1.00)	0.628 (1.00)	0.268 (1.00)	0.0188 (1.00)
20p loss	33 (8%)	375	0.206 (1.00)	0.0399 (1.00)	0.251 (1.00)	0.0376 (1.00)	1 (1.00)	0.917 (1.00)	0.795 (1.00)	0.957 (1.00)	0.401 (1.00)	0.304 (1.00)
20q loss	16 (4%)	392	0.0956 (1.00)	0.0473 (1.00)	0.736 (1.00)	0.46 (1.00)	0.486 (1.00)	0.531 (1.00)	0.455 (1.00)	0.64 (1.00)	0.402 (1.00)	0.751 (1.00)
21q loss	77 (19%)	331	0.0344 (1.00)	0.101 (1.00)	0.0684 (1.00)	0.33 (1.00)	0.00256 (1.00)	0.011 (1.00)	0.173 (1.00)	0.127 (1.00)	0.00281 (1.00)	0.0183 (1.00)
xq loss	78 (19%)	330	0.00638 (1.00)	0.256 (1.00)	0.971 (1.00)	0.816 (1.00)	0.702 (1.00)	0.579 (1.00)	0.0697 (1.00)	0.275 (1.00)	0.0227 (1.00)	0.0127 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.03

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
1P GAIN MUTATED	19	37	17	16
1P GAIN WILD-TYPE	68	66	139	46

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S2. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
2P GAIN MUTATED	42	41	12	15
2P GAIN WILD-TYPE	45	62	144	47

Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.21

Table S3. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
2P GAIN MUTATED	48	49	7
2P GAIN WILD-TYPE	110	88	61

Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S4. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
2Q GAIN MUTATED	24	19	8	4
2Q GAIN WILD-TYPE	63	84	148	58

Figure S4. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.22

Table S5. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
3P GAIN MUTATED	27	25	36	23	2	22
3P GAIN WILD-TYPE	47	21	57	43	29	62

Figure S5. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.03

Table S6. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
3Q GAIN MUTATED	45	61	46	26
3Q GAIN WILD-TYPE	42	42	110	36

Figure S6. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S7. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
3Q GAIN MUTATED	30	30	49	31	3	29
3Q GAIN WILD-TYPE	44	16	44	35	28	55

Figure S7. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S8. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
5P GAIN MUTATED	39	54	33	40
5P GAIN WILD-TYPE	48	49	123	22

Figure S8. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S9. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
7P GAIN MUTATED	51	56	32	33
7P GAIN WILD-TYPE	36	47	124	29

Figure S9. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.18

Table S10. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
7P GAIN MUTATED	24	18	45	31	3	44
7P GAIN WILD-TYPE	50	28	48	35	28	40

Figure S10. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S11. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
7Q GAIN MUTATED	48	45	32	25
7Q GAIN WILD-TYPE	39	58	124	37

Figure S11. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S12. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
9P GAIN MUTATED	11	22	9	26
9P GAIN WILD-TYPE	76	81	147	36

Figure S12. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.045

Table S13. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9P GAIN MUTATED	32	5	14	14
9P GAIN WILD-TYPE	66	38	120	105

Figure S13. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S14. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9P GAIN MUTATED	13	6	13	2	1	30
9P GAIN WILD-TYPE	61	40	80	64	30	54

Figure S14. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.038

Table S15. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
9Q GAIN MUTATED	9	16	11	20
9Q GAIN WILD-TYPE	78	87	145	42

Figure S15. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S16. Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9Q GAIN MUTATED	9	6	10	2	0	26
9Q GAIN WILD-TYPE	65	40	83	64	31	58

Figure S16. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S17. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
10P GAIN MUTATED	43	40	14	20
10P GAIN WILD-TYPE	44	63	142	42

Figure S17. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.16

Table S18. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
10Q GAIN MUTATED	18	15	6	5
10Q GAIN WILD-TYPE	69	88	150	57

Figure S18. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S19. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
12P GAIN MUTATED	38	32	25	20
12P GAIN WILD-TYPE	49	71	131	42

Figure S19. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S20. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
18P GAIN MUTATED	27	44	13	32
18P GAIN WILD-TYPE	60	59	143	30

Figure S20. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.038

Table S21. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
18P GAIN MUTATED	15	10	36	21	0	30
18P GAIN WILD-TYPE	59	36	57	45	31	54

Figure S21. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.24

Table S22. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
19P GAIN MUTATED	17	38	22	11
19P GAIN WILD-TYPE	70	65	134	51

Figure S22. 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 = 0.008

Table S23. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
19Q GAIN MUTATED	42	49	29	15
19Q GAIN WILD-TYPE	45	54	127	47

Figure S23. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S24. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
20P GAIN MUTATED	50	57	54	41
20P GAIN WILD-TYPE	37	46	102	21

Figure S24. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S25. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
20Q GAIN MUTATED	60	68	61	41
20Q GAIN WILD-TYPE	27	35	95	21

Figure S25. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S26. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
21Q GAIN MUTATED	28	54	20	15
21Q GAIN WILD-TYPE	59	49	136	47

Figure S26. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.19

Table S27. Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
2Q LOSS MUTATED	25	26	18	21
2Q LOSS WILD-TYPE	62	77	138	41

Figure S27. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S28. Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
3P LOSS MUTATED	4	9	27
3P LOSS WILD-TYPE	94	150	69

Figure S28. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S29. Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
3P LOSS MUTATED	2	7	26	5
3P LOSS WILD-TYPE	99	107	52	55

Figure S29. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S30. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
3P LOSS MUTATED	26	1	15	8
3P LOSS WILD-TYPE	72	42	119	111

Figure S30. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.11

Table S31. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
3P LOSS MUTATED	2	2	15	10	1	20
3P LOSS WILD-TYPE	72	44	78	56	30	64

Figure S31. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S32. Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
4P LOSS MUTATED	37	47	24	34
4P LOSS WILD-TYPE	50	56	132	28

Figure S32. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S33. Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
4Q LOSS MUTATED	35	42	23	36
4Q LOSS WILD-TYPE	52	61	133	26

Figure S33. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S34. Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
5Q LOSS MUTATED	48	49	32	30
5Q LOSS WILD-TYPE	39	54	124	32

Figure S34. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S35. Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
6P LOSS MUTATED	40	29	16	15
6P LOSS WILD-TYPE	47	74	140	47

Figure S35. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.2

Table S36. Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
6P LOSS MUTATED	25	49	14
6P LOSS WILD-TYPE	133	88	54

Figure S36. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S37. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
6Q LOSS MUTATED	63	46	22	25
6Q LOSS WILD-TYPE	24	57	134	37

Figure S37. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.038

Table S38. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
6Q LOSS MUTATED	26	23	46	31	2	25
6Q LOSS WILD-TYPE	48	23	47	35	29	59

Figure S38. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S39. Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
8P LOSS MUTATED	30	66	47	42
8P LOSS WILD-TYPE	57	37	109	20

Figure S39. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S40. Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
9P LOSS MUTATED	48	49	72	5
9P LOSS WILD-TYPE	39	54	84	57

Figure S40. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S41. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9P LOSS MUTATED	23	24	70	53
9P LOSS WILD-TYPE	75	19	64	66

Figure S41. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S42. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9P LOSS MUTATED	24	24	43	39	21	19
9P LOSS WILD-TYPE	50	22	50	27	10	65

Figure S42. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S43. Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
9Q LOSS MUTATED	47	43	74	5
9Q LOSS WILD-TYPE	40	60	82	57

Figure S43. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.03

Table S44. Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
9Q LOSS MUTATED	46	74	35
9Q LOSS WILD-TYPE	112	63	33

Figure S44. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S45. Gene #58: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	114	78	60
9Q LOSS MUTATED	56	60	20	14
9Q LOSS WILD-TYPE	45	54	58	46

Figure S45. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S46. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
9Q LOSS MUTATED	17	24	76	49
9Q LOSS WILD-TYPE	81	19	58	70

Figure S46. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S47. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
9Q LOSS MUTATED	28	23	43	35	25	12
9Q LOSS WILD-TYPE	46	23	50	31	6	72

Figure S47. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S48. Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
10Q LOSS MUTATED	31	48	22	26
10Q LOSS WILD-TYPE	56	55	134	36

Figure S48. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.17

Table S49. Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
10Q LOSS MUTATED	41	60	13
10Q LOSS WILD-TYPE	117	77	55

Figure S49. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S50. Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
11P LOSS MUTATED	53	64	49	14
11P LOSS WILD-TYPE	34	39	107	48

Figure S50. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S51. Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
11P LOSS MUTATED	42	81	34
11P LOSS WILD-TYPE	116	56	34

Figure S51. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.082

Table S52. Gene #61: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	159	96
11P LOSS MUTATED	34	88	30
11P LOSS WILD-TYPE	64	71	66

Figure S52. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.17

Table S53. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	43	134	119
11P LOSS MUTATED	25	22	70	57
11P LOSS WILD-TYPE	73	21	64	62

Figure S53. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S54. Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
11Q LOSS MUTATED	42	45	29	15
11Q LOSS WILD-TYPE	45	58	127	47

Figure S54. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S55. Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
12Q LOSS MUTATED	16	13	9	19
12Q LOSS WILD-TYPE	71	90	147	43

Figure S55. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.22

Table S56. Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
13Q LOSS MUTATED	23	30	16	16
13Q LOSS WILD-TYPE	64	73	140	46

Figure S56. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S57. Gene #65: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
13Q LOSS MUTATED	28	28	8	18	3
13Q LOSS WILD-TYPE	61	71	85	52	51

Figure S57. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S58. Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
14Q LOSS MUTATED	30	52	25	12
14Q LOSS WILD-TYPE	57	51	131	50

Figure S58. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.045

Table S59. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
14Q LOSS MUTATED	19	20	32	28	1	16
14Q LOSS WILD-TYPE	55	26	61	38	30	68

Figure S59. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S60. Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
15Q LOSS MUTATED	36	55	22	31
15Q LOSS WILD-TYPE	51	48	134	31

Figure S60. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.24

Table S61. Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	137	68
15Q LOSS MUTATED	64	51	10
15Q LOSS WILD-TYPE	94	86	58

Figure S61. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S62. Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	89	99	93	70	54
15Q LOSS MUTATED	29	49	17	34	15
15Q LOSS WILD-TYPE	60	50	76	36	39

Figure S62. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.097

Table S63. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
15Q LOSS MUTATED	23	23	37	21	1	35
15Q LOSS WILD-TYPE	51	23	56	45	30	49

Figure S63. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S64. Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
16P LOSS MUTATED	27	28	13	38
16P LOSS WILD-TYPE	60	75	143	24

Figure S64. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S65. Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
16Q LOSS MUTATED	30	34	8	32
16Q LOSS WILD-TYPE	57	69	148	30

Figure S65. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S66. Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
17P LOSS MUTATED	60	50	50	22
17P LOSS WILD-TYPE	27	53	106	40

Figure S66. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S67. Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	87	103	156	62
22Q LOSS MUTATED	27	59	25	48
22Q LOSS WILD-TYPE	60	44	131	14

Figure S67. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S68. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	74	46	93	66	31	84
22Q LOSS MUTATED	23	14	44	30	1	42
22Q LOSS WILD-TYPE	51	32	49	36	30	42

Figure S68. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt
Number of patients = 408
Number of significantly arm-level cnvs = 80
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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