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)