Correlation between copy number variations of arm-level result and molecular subtypes
Ovarian Serous Cystadenocarcinoma (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/C15B01CD
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 14 molecular subtypes across 579 patients, 42 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 2q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 5p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 5q loss cnv correlated to 'METHLYATION_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'METHLYATION_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

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 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 42 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
MIR
CNMF
MIR
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
2p gain 186 (32%) 393 1e-05
(0.011)
2e-05
(0.0215)
0.886
(1.00)
0.00052
(0.542)
1e-05
(0.011)
1e-05
(0.011)
0.0357
(1.00)
0.0778
(1.00)
0.00016
(0.17)
0.00178
(1.00)
0.822
(1.00)
0.0255
(1.00)
0.675
(1.00)
0.608
(1.00)
20q gain 328 (57%) 251 3e-05
(0.0321)
0.00024
(0.253)
0.668
(1.00)
8e-05
(0.0852)
1e-05
(0.011)
1e-05
(0.011)
0.66
(1.00)
0.0822
(1.00)
0.00915
(1.00)
0.138
(1.00)
0.257
(1.00)
0.00516
(1.00)
1
(1.00)
0.495
(1.00)
2q gain 155 (27%) 424 0.00057
(0.592)
7e-05
(0.0746)
1
(1.00)
0.00739
(1.00)
1e-05
(0.011)
0.00023
(0.243)
0.109
(1.00)
0.322
(1.00)
0.00368
(1.00)
0.0204
(1.00)
0.609
(1.00)
0.00653
(1.00)
1
(1.00)
0.746
(1.00)
12p gain 255 (44%) 324 0.0001
(0.106)
0.00154
(1.00)
0.741
(1.00)
0.001
(1.00)
1e-05
(0.011)
1e-05
(0.011)
0.305
(1.00)
0.317
(1.00)
0.00054
(0.562)
0.00378
(1.00)
0.226
(1.00)
0.00026
(0.274)
0.415
(1.00)
0.251
(1.00)
15q loss 280 (48%) 299 0.00049
(0.511)
0.0163
(1.00)
8e-05
(0.0852)
0.00032
(0.336)
1e-05
(0.011)
1e-05
(0.011)
0.378
(1.00)
0.813
(1.00)
0.0662
(1.00)
0.612
(1.00)
0.00813
(1.00)
0.00063
(0.654)
0.0427
(1.00)
0.623
(1.00)
6p gain 170 (29%) 409 0.513
(1.00)
0.0042
(1.00)
0.904
(1.00)
0.0134
(1.00)
1e-05
(0.011)
9e-05
(0.0957)
0.864
(1.00)
0.23
(1.00)
0.159
(1.00)
0.00798
(1.00)
0.361
(1.00)
0.0645
(1.00)
0.415
(1.00)
0.762
(1.00)
6q gain 97 (17%) 482 0.66
(1.00)
0.0517
(1.00)
0.821
(1.00)
0.0221
(1.00)
1e-05
(0.011)
1e-05
(0.011)
0.789
(1.00)
0.997
(1.00)
0.00475
(1.00)
0.0218
(1.00)
0.197
(1.00)
0.0295
(1.00)
0.381
(1.00)
0.576
(1.00)
10p gain 188 (32%) 391 0.00417
(1.00)
0.0217
(1.00)
0.678
(1.00)
0.376
(1.00)
1e-05
(0.011)
0.00021
(0.222)
0.979
(1.00)
0.00947
(1.00)
0.0107
(1.00)
0.125
(1.00)
0.557
(1.00)
0.00066
(0.684)
1
(1.00)
0.941
(1.00)
12q gain 177 (31%) 402 0.0046
(1.00)
0.0565
(1.00)
0.626
(1.00)
0.0341
(1.00)
1e-05
(0.011)
2e-05
(0.0215)
0.019
(1.00)
0.221
(1.00)
0.00192
(1.00)
0.009
(1.00)
0.102
(1.00)
0.0105
(1.00)
0.0743
(1.00)
0.29
(1.00)
13q gain 60 (10%) 519 0.00741
(1.00)
0.00035
(0.367)
0.586
(1.00)
0.025
(1.00)
6e-05
(0.0641)
3e-05
(0.0321)
0.492
(1.00)
0.409
(1.00)
0.23
(1.00)
0.427
(1.00)
0.151
(1.00)
0.0987
(1.00)
0.455
(1.00)
20p gain 289 (50%) 290 0.00142
(1.00)
0.0011
(1.00)
0.723
(1.00)
0.00029
(0.305)
1e-05
(0.011)
1e-05
(0.011)
0.332
(1.00)
0.371
(1.00)
0.00373
(1.00)
0.166
(1.00)
0.225
(1.00)
0.00341
(1.00)
0.391
(1.00)
0.524
(1.00)
1q gain 221 (38%) 358 0.832
(1.00)
0.269
(1.00)
0.705
(1.00)
0.227
(1.00)
1e-05
(0.011)
0.00864
(1.00)
0.502
(1.00)
0.548
(1.00)
0.435
(1.00)
0.277
(1.00)
0.229
(1.00)
0.106
(1.00)
0.198
(1.00)
0.562
(1.00)
3q gain 275 (47%) 304 0.934
(1.00)
0.867
(1.00)
0.344
(1.00)
0.427
(1.00)
1e-05
(0.011)
0.0163
(1.00)
0.639
(1.00)
0.258
(1.00)
0.694
(1.00)
0.927
(1.00)
0.253
(1.00)
0.0893
(1.00)
1
(1.00)
0.635
(1.00)
7p gain 181 (31%) 398 0.589
(1.00)
0.475
(1.00)
0.0848
(1.00)
0.108
(1.00)
1e-05
(0.011)
0.00025
(0.264)
0.646
(1.00)
0.5
(1.00)
0.53
(1.00)
0.683
(1.00)
0.966
(1.00)
0.119
(1.00)
1
(1.00)
0.762
(1.00)
7q gain 203 (35%) 376 0.651
(1.00)
0.0846
(1.00)
0.3
(1.00)
0.38
(1.00)
1e-05
(0.011)
0.00156
(1.00)
0.46
(1.00)
0.248
(1.00)
0.925
(1.00)
0.643
(1.00)
0.151
(1.00)
0.628
(1.00)
0.646
(1.00)
0.369
(1.00)
19p gain 171 (30%) 408 0.0757
(1.00)
0.452
(1.00)
0.517
(1.00)
0.115
(1.00)
2e-05
(0.0215)
0.0265
(1.00)
0.0566
(1.00)
0.324
(1.00)
0.19
(1.00)
0.579
(1.00)
0.269
(1.00)
0.31
(1.00)
1
(1.00)
0.744
(1.00)
19q gain 161 (28%) 418 0.259
(1.00)
0.753
(1.00)
0.907
(1.00)
0.169
(1.00)
6e-05
(0.0641)
0.133
(1.00)
0.476
(1.00)
0.462
(1.00)
0.205
(1.00)
0.438
(1.00)
0.271
(1.00)
0.674
(1.00)
0.594
(1.00)
0.722
(1.00)
5p loss 133 (23%) 446 0.0747
(1.00)
0.0313
(1.00)
0.539
(1.00)
0.0873
(1.00)
0.0124
(1.00)
0.00702
(1.00)
0.0887
(1.00)
0.0573
(1.00)
0.00018
(0.191)
0.047
(1.00)
0.569
(1.00)
0.0499
(1.00)
1
(1.00)
0.905
(1.00)
5q loss 223 (39%) 356 0.00042
(0.439)
0.00159
(1.00)
0.708
(1.00)
0.0129
(1.00)
0.00042
(0.439)
1e-05
(0.011)
0.034
(1.00)
0.0936
(1.00)
0.0011
(1.00)
0.147
(1.00)
0.62
(1.00)
0.00675
(1.00)
0.378
(1.00)
0.719
(1.00)
9q loss 286 (49%) 293 0.00713
(1.00)
0.013
(1.00)
0.222
(1.00)
0.0344
(1.00)
1e-05
(0.011)
0.00538
(1.00)
0.609
(1.00)
0.682
(1.00)
0.00734
(1.00)
0.0517
(1.00)
0.226
(1.00)
0.0576
(1.00)
1
(1.00)
0.625
(1.00)
13q loss 310 (54%) 269 0.0297
(1.00)
0.00822
(1.00)
0.804
(1.00)
0.0175
(1.00)
0.0515
(1.00)
1e-05
(0.011)
0.00566
(1.00)
0.344
(1.00)
0.467
(1.00)
0.42
(1.00)
0.217
(1.00)
0.535
(1.00)
0.666
(1.00)
0.15
(1.00)
14q loss 215 (37%) 364 0.25
(1.00)
0.191
(1.00)
0.967
(1.00)
0.398
(1.00)
1e-05
(0.011)
0.00367
(1.00)
0.981
(1.00)
0.607
(1.00)
0.00374
(1.00)
0.0482
(1.00)
0.855
(1.00)
0.402
(1.00)
0.381
(1.00)
0.224
(1.00)
22q loss 430 (74%) 149 0.00242
(1.00)
0.093
(1.00)
0.0369
(1.00)
0.127
(1.00)
0.00015
(0.159)
0.00194
(1.00)
0.0855
(1.00)
0.0239
(1.00)
0.0863
(1.00)
0.129
(1.00)
0.0411
(1.00)
0.574
(1.00)
0.135
(1.00)
0.107
(1.00)
1p gain 168 (29%) 411 0.0804
(1.00)
0.349
(1.00)
0.122
(1.00)
0.73
(1.00)
0.00038
(0.398)
0.183
(1.00)
0.105
(1.00)
0.263
(1.00)
0.611
(1.00)
0.949
(1.00)
0.252
(1.00)
0.683
(1.00)
0.231
(1.00)
0.525
(1.00)
3p gain 160 (28%) 419 0.437
(1.00)
0.449
(1.00)
0.07
(1.00)
0.528
(1.00)
0.0116
(1.00)
0.786
(1.00)
1
(1.00)
0.383
(1.00)
0.66
(1.00)
0.687
(1.00)
0.991
(1.00)
0.819
(1.00)
1
(1.00)
0.812
(1.00)
4p gain 60 (10%) 519 0.246
(1.00)
0.192
(1.00)
0.00499
(1.00)
0.0608
(1.00)
0.017
(1.00)
0.119
(1.00)
0.461
(1.00)
0.395
(1.00)
0.606
(1.00)
0.84
(1.00)
0.323
(1.00)
0.018
(1.00)
1
(1.00)
0.572
(1.00)
4q gain 32 (6%) 547 0.494
(1.00)
0.764
(1.00)
0.212
(1.00)
0.08
(1.00)
0.00461
(1.00)
0.00775
(1.00)
0.35
(1.00)
0.226
(1.00)
0.763
(1.00)
0.857
(1.00)
0.227
(1.00)
0.064
(1.00)
5p gain 199 (34%) 380 0.567
(1.00)
0.71
(1.00)
0.855
(1.00)
0.762
(1.00)
0.00041
(0.429)
0.194
(1.00)
0.495
(1.00)
0.0721
(1.00)
0.127
(1.00)
0.54
(1.00)
0.179
(1.00)
0.575
(1.00)
0.666
(1.00)
0.216
(1.00)
5q gain 60 (10%) 519 0.0589
(1.00)
0.196
(1.00)
0.822
(1.00)
0.892
(1.00)
0.845
(1.00)
0.496
(1.00)
0.464
(1.00)
0.369
(1.00)
0.71
(1.00)
0.407
(1.00)
0.382
(1.00)
0.791
(1.00)
0.481
(1.00)
8p gain 119 (21%) 460 0.0679
(1.00)
0.0038
(1.00)
0.399
(1.00)
0.421
(1.00)
0.693
(1.00)
0.808
(1.00)
0.137
(1.00)
0.00336
(1.00)
0.618
(1.00)
1
(1.00)
0.133
(1.00)
0.493
(1.00)
0.221
(1.00)
0.101
(1.00)
8q gain 242 (42%) 337 0.0207
(1.00)
0.00064
(0.664)
0.0807
(1.00)
0.141
(1.00)
0.259
(1.00)
0.448
(1.00)
0.319
(1.00)
0.267
(1.00)
0.0299
(1.00)
0.0853
(1.00)
0.56
(1.00)
0.863
(1.00)
0.031
(1.00)
0.686
(1.00)
9p gain 92 (16%) 487 0.113
(1.00)
0.423
(1.00)
0.237
(1.00)
0.867
(1.00)
0.00273
(1.00)
0.00847
(1.00)
0.4
(1.00)
0.726
(1.00)
0.692
(1.00)
0.412
(1.00)
0.186
(1.00)
0.188
(1.00)
0.624
(1.00)
0.608
(1.00)
9q gain 45 (8%) 534 0.252
(1.00)
0.309
(1.00)
0.0926
(1.00)
0.533
(1.00)
0.138
(1.00)
0.224
(1.00)
0.579
(1.00)
0.0268
(1.00)
0.483
(1.00)
0.0914
(1.00)
0.496
(1.00)
0.752
(1.00)
0.455
(1.00)
10q gain 111 (19%) 468 0.00423
(1.00)
0.00911
(1.00)
0.24
(1.00)
0.117
(1.00)
0.00393
(1.00)
0.0935
(1.00)
0.768
(1.00)
0.0615
(1.00)
0.105
(1.00)
0.22
(1.00)
0.731
(1.00)
0.247
(1.00)
0.646
(1.00)
0.659
(1.00)
11p gain 77 (13%) 502 0.713
(1.00)
0.1
(1.00)
0.64
(1.00)
0.468
(1.00)
0.136
(1.00)
0.0138
(1.00)
0.0278
(1.00)
0.0262
(1.00)
0.0581
(1.00)
0.0348
(1.00)
0.559
(1.00)
0.838
(1.00)
1
(1.00)
11q gain 115 (20%) 464 0.394
(1.00)
0.251
(1.00)
0.883
(1.00)
0.181
(1.00)
0.0044
(1.00)
0.00187
(1.00)
0.206
(1.00)
0.00079
(0.817)
0.303
(1.00)
0.156
(1.00)
0.409
(1.00)
0.779
(1.00)
0.323
(1.00)
0.106
(1.00)
14q gain 59 (10%) 520 0.139
(1.00)
0.191
(1.00)
0.405
(1.00)
0.699
(1.00)
0.411
(1.00)
0.741
(1.00)
0.33
(1.00)
0.172
(1.00)
0.503
(1.00)
0.568
(1.00)
0.656
(1.00)
0.63
(1.00)
1
(1.00)
15q gain 40 (7%) 539 0.848
(1.00)
0.479
(1.00)
0.0876
(1.00)
0.758
(1.00)
0.0976
(1.00)
0.604
(1.00)
0.114
(1.00)
0.109
(1.00)
0.738
(1.00)
0.931
(1.00)
0.314
(1.00)
0.203
(1.00)
1
(1.00)
16p gain 59 (10%) 520 0.00232
(1.00)
0.00505
(1.00)
0.405
(1.00)
0.175
(1.00)
0.0296
(1.00)
0.0176
(1.00)
0.348
(1.00)
0.0347
(1.00)
0.65
(1.00)
0.799
(1.00)
0.122
(1.00)
0.08
(1.00)
0.481
(1.00)
16q gain 31 (5%) 548 0.00095
(0.979)
0.0438
(1.00)
0.162
(1.00)
0.221
(1.00)
0.268
(1.00)
0.00319
(1.00)
0.455
(1.00)
0.026
(1.00)
1
(1.00)
0.364
(1.00)
0.00073
(0.756)
0.105
(1.00)
1
(1.00)
17p gain 22 (4%) 557 0.431
(1.00)
0.113
(1.00)
0.0552
(1.00)
0.0525
(1.00)
0.154
(1.00)
0.231
(1.00)
0.499
(1.00)
0.406
(1.00)
0.211
(1.00)
0.00371
(1.00)
0.174
(1.00)
0.838
(1.00)
17q gain 47 (8%) 532 0.423
(1.00)
0.0378
(1.00)
0.758
(1.00)
0.0369
(1.00)
0.522
(1.00)
0.389
(1.00)
0.588
(1.00)
0.373
(1.00)
0.902
(1.00)
0.0227
(1.00)
0.823
(1.00)
0.879
(1.00)
1
(1.00)
18p gain 120 (21%) 459 0.184
(1.00)
0.0984
(1.00)
0.871
(1.00)
0.392
(1.00)
0.00153
(1.00)
0.0003
(0.316)
0.0238
(1.00)
0.111
(1.00)
0.812
(1.00)
0.69
(1.00)
0.35
(1.00)
0.234
(1.00)
0.646
(1.00)
0.812
(1.00)
18q gain 72 (12%) 507 0.644
(1.00)
0.166
(1.00)
0.231
(1.00)
0.39
(1.00)
0.0236
(1.00)
0.0244
(1.00)
0.514
(1.00)
0.397
(1.00)
0.484
(1.00)
0.271
(1.00)
0.107
(1.00)
0.194
(1.00)
1
(1.00)
1
(1.00)
21q gain 109 (19%) 470 0.291
(1.00)
0.879
(1.00)
0.962
(1.00)
0.582
(1.00)
0.00169
(1.00)
0.0163
(1.00)
0.456
(1.00)
0.393
(1.00)
0.335
(1.00)
0.843
(1.00)
0.0229
(1.00)
0.044
(1.00)
1
(1.00)
22q gain 24 (4%) 555 0.367
(1.00)
0.6
(1.00)
0.932
(1.00)
0.605
(1.00)
0.368
(1.00)
0.17
(1.00)
0.392
(1.00)
0.375
(1.00)
0.563
(1.00)
0.608
(1.00)
0.0968
(1.00)
0.0815
(1.00)
0.571
(1.00)
0.382
(1.00)
xq gain 106 (18%) 473 0.482
(1.00)
0.828
(1.00)
0.843
(1.00)
0.267
(1.00)
0.00048
(0.501)
0.933
(1.00)
0.311
(1.00)
0.837
(1.00)
0.762
(1.00)
0.93
(1.00)
0.474
(1.00)
0.3
(1.00)
1
(1.00)
0.908
(1.00)
1p loss 65 (11%) 514 0.0322
(1.00)
0.00033
(0.346)
0.465
(1.00)
0.195
(1.00)
0.467
(1.00)
0.291
(1.00)
0.0207
(1.00)
0.211
(1.00)
0.632
(1.00)
0.508
(1.00)
0.446
(1.00)
0.309
(1.00)
1
(1.00)
1q loss 43 (7%) 536 0.118
(1.00)
0.0144
(1.00)
0.0581
(1.00)
0.601
(1.00)
0.69
(1.00)
0.383
(1.00)
0.222
(1.00)
0.619
(1.00)
0.466
(1.00)
1
(1.00)
0.969
(1.00)
0.932
(1.00)
2p loss 53 (9%) 526 0.931
(1.00)
0.0238
(1.00)
0.617
(1.00)
0.489
(1.00)
0.578
(1.00)
0.775
(1.00)
0.484
(1.00)
0.894
(1.00)
0.335
(1.00)
0.816
(1.00)
0.722
(1.00)
0.402
(1.00)
0.481
(1.00)
2q loss 59 (10%) 520 0.919
(1.00)
0.27
(1.00)
0.697
(1.00)
0.151
(1.00)
0.855
(1.00)
0.682
(1.00)
0.89
(1.00)
0.938
(1.00)
0.499
(1.00)
0.794
(1.00)
0.556
(1.00)
0.23
(1.00)
0.481
(1.00)
3p loss 95 (16%) 484 0.0228
(1.00)
0.00084
(0.867)
0.818
(1.00)
0.00584
(1.00)
0.00055
(0.572)
0.00276
(1.00)
0.65
(1.00)
0.267
(1.00)
0.0621
(1.00)
0.00559
(1.00)
0.122
(1.00)
0.0912
(1.00)
1
(1.00)
0.124
(1.00)
3q loss 43 (7%) 536 0.0134
(1.00)
0.0395
(1.00)
0.286
(1.00)
0.0576
(1.00)
0.0296
(1.00)
0.00292
(1.00)
0.933
(1.00)
0.361
(1.00)
0.231
(1.00)
0.0917
(1.00)
0.305
(1.00)
0.00112
(1.00)
0.594
(1.00)
0.0333
(1.00)
4p loss 316 (55%) 263 0.366
(1.00)
0.0232
(1.00)
0.282
(1.00)
0.615
(1.00)
0.00416
(1.00)
0.482
(1.00)
0.15
(1.00)
0.132
(1.00)
0.426
(1.00)
0.441
(1.00)
0.12
(1.00)
0.197
(1.00)
1
(1.00)
0.624
(1.00)
4q loss 362 (63%) 217 0.208
(1.00)
0.0819
(1.00)
0.5
(1.00)
0.716
(1.00)
0.00127
(1.00)
0.561
(1.00)
0.121
(1.00)
0.0179
(1.00)
0.269
(1.00)
0.35
(1.00)
0.214
(1.00)
0.181
(1.00)
1
(1.00)
0.368
(1.00)
6p loss 165 (28%) 414 0.97
(1.00)
0.0201
(1.00)
0.45
(1.00)
0.507
(1.00)
0.147
(1.00)
0.12
(1.00)
0.78
(1.00)
0.849
(1.00)
0.41
(1.00)
0.043
(1.00)
0.48
(1.00)
0.102
(1.00)
0.571
(1.00)
0.574
(1.00)
6q loss 242 (42%) 337 0.962
(1.00)
0.0762
(1.00)
0.433
(1.00)
0.0972
(1.00)
0.0341
(1.00)
0.0712
(1.00)
0.624
(1.00)
0.658
(1.00)
0.019
(1.00)
0.0207
(1.00)
0.792
(1.00)
0.571
(1.00)
0.594
(1.00)
0.902
(1.00)
7p loss 121 (21%) 458 0.991
(1.00)
0.404
(1.00)
0.479
(1.00)
0.699
(1.00)
0.111
(1.00)
0.149
(1.00)
0.541
(1.00)
0.328
(1.00)
0.775
(1.00)
0.712
(1.00)
0.538
(1.00)
0.8
(1.00)
0.594
(1.00)
0.202
(1.00)
7q loss 81 (14%) 498 0.336
(1.00)
0.089
(1.00)
0.347
(1.00)
0.3
(1.00)
0.737
(1.00)
0.11
(1.00)
0.82
(1.00)
0.0696
(1.00)
0.478
(1.00)
0.312
(1.00)
0.124
(1.00)
0.82
(1.00)
1
(1.00)
0.338
(1.00)
8p loss 277 (48%) 302 0.741
(1.00)
0.89
(1.00)
0.242
(1.00)
0.946
(1.00)
0.00241
(1.00)
0.11
(1.00)
0.119
(1.00)
0.297
(1.00)
0.481
(1.00)
0.703
(1.00)
0.701
(1.00)
0.037
(1.00)
1
(1.00)
0.94
(1.00)
8q loss 90 (16%) 489 0.00762
(1.00)
0.00521
(1.00)
0.519
(1.00)
0.263
(1.00)
0.00106
(1.00)
0.0346
(1.00)
0.0217
(1.00)
0.234
(1.00)
0.00095
(0.979)
0.0288
(1.00)
0.663
(1.00)
0.124
(1.00)
1
(1.00)
0.901
(1.00)
9p loss 262 (45%) 317 0.00323
(1.00)
0.00598
(1.00)
0.51
(1.00)
0.183
(1.00)
0.0162
(1.00)
0.0691
(1.00)
0.793
(1.00)
0.546
(1.00)
0.899
(1.00)
0.107
(1.00)
0.0546
(1.00)
0.254
(1.00)
0.391
(1.00)
0.154
(1.00)
10p loss 97 (17%) 482 0.223
(1.00)
0.963
(1.00)
0.221
(1.00)
0.336
(1.00)
0.643
(1.00)
0.232
(1.00)
0.594
(1.00)
0.0878
(1.00)
0.652
(1.00)
0.555
(1.00)
0.359
(1.00)
0.833
(1.00)
1
(1.00)
0.221
(1.00)
10q loss 124 (21%) 455 0.938
(1.00)
0.825
(1.00)
0.00449
(1.00)
0.296
(1.00)
0.0229
(1.00)
0.00188
(1.00)
0.302
(1.00)
0.407
(1.00)
0.773
(1.00)
0.741
(1.00)
0.693
(1.00)
0.371
(1.00)
0.381
(1.00)
0.695
(1.00)
11p loss 198 (34%) 381 0.239
(1.00)
0.0109
(1.00)
0.545
(1.00)
0.31
(1.00)
0.199
(1.00)
0.0367
(1.00)
0.1
(1.00)
0.611
(1.00)
0.0408
(1.00)
0.11
(1.00)
0.472
(1.00)
0.143
(1.00)
0.323
(1.00)
0.802
(1.00)
11q loss 148 (26%) 431 0.296
(1.00)
0.902
(1.00)
0.211
(1.00)
0.561
(1.00)
0.00946
(1.00)
0.07
(1.00)
0.423
(1.00)
0.767
(1.00)
0.269
(1.00)
0.801
(1.00)
0.495
(1.00)
0.176
(1.00)
0.594
(1.00)
0.384
(1.00)
12p loss 79 (14%) 500 0.00262
(1.00)
0.011
(1.00)
0.657
(1.00)
0.00649
(1.00)
0.00104
(1.00)
0.254
(1.00)
0.87
(1.00)
0.152
(1.00)
0.315
(1.00)
0.201
(1.00)
0.00955
(1.00)
0.00618
(1.00)
0.293
(1.00)
0.725
(1.00)
12q loss 105 (18%) 474 0.0826
(1.00)
0.0831
(1.00)
0.728
(1.00)
0.17
(1.00)
0.0223
(1.00)
0.223
(1.00)
0.266
(1.00)
0.558
(1.00)
0.173
(1.00)
0.149
(1.00)
0.0259
(1.00)
0.0304
(1.00)
0.135
(1.00)
0.0412
(1.00)
16p loss 334 (58%) 245 0.38
(1.00)
0.846
(1.00)
0.0402
(1.00)
0.351
(1.00)
0.217
(1.00)
0.115
(1.00)
0.766
(1.00)
0.227
(1.00)
0.0397
(1.00)
0.246
(1.00)
0.0483
(1.00)
0.0683
(1.00)
0.675
(1.00)
0.368
(1.00)
16q loss 413 (71%) 166 0.579
(1.00)
0.87
(1.00)
0.00285
(1.00)
0.0795
(1.00)
0.0282
(1.00)
0.0645
(1.00)
0.907
(1.00)
0.308
(1.00)
0.196
(1.00)
0.37
(1.00)
0.0541
(1.00)
0.129
(1.00)
0.624
(1.00)
0.606
(1.00)
17p loss 478 (83%) 101 0.337
(1.00)
0.228
(1.00)
0.136
(1.00)
0.205
(1.00)
0.592
(1.00)
0.249
(1.00)
0.554
(1.00)
0.189
(1.00)
0.102
(1.00)
0.0571
(1.00)
0.474
(1.00)
0.476
(1.00)
1
(1.00)
17q loss 383 (66%) 196 0.0844
(1.00)
0.0283
(1.00)
0.0149
(1.00)
0.0116
(1.00)
0.944
(1.00)
0.557
(1.00)
0.57
(1.00)
0.294
(1.00)
0.534
(1.00)
0.097
(1.00)
0.0776
(1.00)
0.713
(1.00)
0.624
(1.00)
0.278
(1.00)
18p loss 235 (41%) 344 0.411
(1.00)
0.952
(1.00)
0.472
(1.00)
0.0214
(1.00)
0.546
(1.00)
0.00218
(1.00)
0.313
(1.00)
0.00672
(1.00)
0.0238
(1.00)
0.114
(1.00)
0.838
(1.00)
0.538
(1.00)
0.666
(1.00)
0.579
(1.00)
18q loss 293 (51%) 286 0.343
(1.00)
0.972
(1.00)
0.296
(1.00)
0.957
(1.00)
0.854
(1.00)
0.104
(1.00)
0.713
(1.00)
0.0354
(1.00)
0.0114
(1.00)
0.0912
(1.00)
0.978
(1.00)
0.779
(1.00)
0.67
(1.00)
0.247
(1.00)
19p loss 185 (32%) 394 0.978
(1.00)
0.454
(1.00)
0.328
(1.00)
0.0437
(1.00)
0.00498
(1.00)
0.0191
(1.00)
0.00972
(1.00)
0.887
(1.00)
0.667
(1.00)
0.313
(1.00)
0.675
(1.00)
0.119
(1.00)
0.0115
(1.00)
0.126
(1.00)
19q loss 178 (31%) 401 0.692
(1.00)
0.246
(1.00)
0.25
(1.00)
0.015
(1.00)
0.00448
(1.00)
0.0728
(1.00)
0.0602
(1.00)
0.678
(1.00)
0.925
(1.00)
0.719
(1.00)
0.3
(1.00)
0.052
(1.00)
0.00535
(1.00)
0.427
(1.00)
20p loss 50 (9%) 529 0.353
(1.00)
0.722
(1.00)
0.222
(1.00)
0.62
(1.00)
0.111
(1.00)
0.469
(1.00)
0.103
(1.00)
0.2
(1.00)
0.0733
(1.00)
0.00338
(1.00)
0.00079
(0.817)
0.27
(1.00)
0.481
(1.00)
20q loss 32 (6%) 547 0.115
(1.00)
0.5
(1.00)
0.0367
(1.00)
0.507
(1.00)
0.442
(1.00)
0.638
(1.00)
0.0486
(1.00)
0.0972
(1.00)
0.133
(1.00)
0.0136
(1.00)
0.136
(1.00)
0.378
(1.00)
0.481
(1.00)
21q loss 199 (34%) 380 0.818
(1.00)
0.0519
(1.00)
0.386
(1.00)
0.185
(1.00)
0.49
(1.00)
0.141
(1.00)
0.652
(1.00)
0.436
(1.00)
0.583
(1.00)
0.408
(1.00)
0.689
(1.00)
0.733
(1.00)
0.162
(1.00)
0.581
(1.00)
xq loss 277 (48%) 302 0.0528
(1.00)
0.186
(1.00)
0.253
(1.00)
0.909
(1.00)
0.00135
(1.00)
0.162
(1.00)
0.328
(1.00)
0.0468
(1.00)
0.508
(1.00)
0.898
(1.00)
0.745
(1.00)
0.415
(1.00)
1
(1.00)
0.289
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
1Q GAIN MUTATED 56 55 110
1Q GAIN WILD-TYPE 115 151 92

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
2P GAIN MUTATED 93 45 36
2P GAIN WILD-TYPE 122 171 90

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2P GAIN MUTATED 77 48 49
2P GAIN WILD-TYPE 233 110 40

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
2P GAIN MUTATED 37 47 102
2P GAIN WILD-TYPE 134 159 100

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2P GAIN MUTATED 83 44 52
2P GAIN WILD-TYPE 89 131 169

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.17

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
2P GAIN MUTATED 31 12 45
2P GAIN WILD-TYPE 69 55 46

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.075

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2Q GAIN MUTATED 70 36 41
2Q GAIN WILD-TYPE 240 122 48

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
2Q GAIN MUTATED 31 40 84
2Q GAIN WILD-TYPE 140 166 118

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.24

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2Q GAIN MUTATED 66 36 49
2Q GAIN WILD-TYPE 106 139 172

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
3Q GAIN MUTATED 58 90 127
3Q GAIN WILD-TYPE 113 116 75

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
6P GAIN MUTATED 29 56 85
6P GAIN WILD-TYPE 142 150 117

Figure S11.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.096

Table S12.  Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
6P GAIN MUTATED 72 39 55
6P GAIN WILD-TYPE 100 136 166

Figure S12.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S13.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
6Q GAIN MUTATED 12 30 55
6Q GAIN WILD-TYPE 159 176 147

Figure S13.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S14.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
6Q GAIN MUTATED 48 16 32
6Q GAIN WILD-TYPE 124 159 189

Figure S14.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S15.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
7P GAIN MUTATED 43 44 94
7P GAIN WILD-TYPE 128 162 108

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
7Q GAIN MUTATED 46 57 100
7Q GAIN WILD-TYPE 125 149 102

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S17.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
10P GAIN MUTATED 41 45 102
10P GAIN WILD-TYPE 130 161 100

Figure S17.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.22

Table S18.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
10P GAIN MUTATED 77 44 63
10P GAIN WILD-TYPE 95 131 158

Figure S18.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
12P GAIN MUTATED 118 75 49
12P GAIN WILD-TYPE 97 141 77

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

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S20.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
12P GAIN MUTATED 54 68 133
12P GAIN WILD-TYPE 117 138 69

Figure S20.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S21.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12P GAIN MUTATED 104 71 74
12P GAIN WILD-TYPE 68 104 147

Figure S21.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S22.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
12Q GAIN MUTATED 40 38 99
12Q GAIN WILD-TYPE 131 168 103

Figure S22.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.021

Table S23.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12Q GAIN MUTATED 78 43 54
12Q GAIN WILD-TYPE 94 132 167

Figure S23.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.064

Table S24.  Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
13Q GAIN MUTATED 22 7 31
13Q GAIN WILD-TYPE 149 199 171

Figure S24.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.032

Table S25.  Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
13Q GAIN MUTATED 31 20 8
13Q GAIN WILD-TYPE 141 155 213

Figure S25.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.021

Table S26.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
19P GAIN MUTATED 33 55 83
19P GAIN WILD-TYPE 138 151 119

Figure S26.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.064

Table S27.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
19Q GAIN MUTATED 33 49 79
19Q GAIN WILD-TYPE 138 157 123

Figure S27.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S28.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
20P GAIN MUTATED 66 79 144
20P GAIN WILD-TYPE 105 127 58

Figure S28.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S29.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20P GAIN MUTATED 117 79 86
20P GAIN WILD-TYPE 55 96 135

Figure S29.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.032

Table S30.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
20Q GAIN MUTATED 143 95 76
20Q GAIN WILD-TYPE 72 121 50

Figure S30.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.085

Table S31.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
20Q GAIN MUTATED 35 30 35 40 24 41 26 21 42 19
20Q GAIN WILD-TYPE 50 27 23 42 10 34 8 15 10 23

Figure S31.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S32.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
20Q GAIN MUTATED 69 98 161
20Q GAIN WILD-TYPE 102 108 41

Figure S32.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S33.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20Q GAIN MUTATED 132 87 101
20Q GAIN WILD-TYPE 40 88 120

Figure S33.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.19

Table S34.  Gene #49: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
5P LOSS MUTATED 21 10 39
5P LOSS WILD-TYPE 79 57 52

Figure S34.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S35.  Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
5Q LOSS MUTATED 96 51 72
5Q LOSS WILD-TYPE 76 124 149

Figure S35.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S36.  Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
9Q LOSS MUTATED 81 68 137
9Q LOSS WILD-TYPE 90 138 65

Figure S36.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S37.  Gene #65: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
13Q LOSS MUTATED 89 72 144
13Q LOSS WILD-TYPE 83 103 77

Figure S37.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S38.  Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
14Q LOSS MUTATED 52 58 105
14Q LOSS WILD-TYPE 119 148 97

Figure S38.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MIR_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.085

Table S39.  Gene #67: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
15Q LOSS MUTATED 62 70 138
15Q LOSS WILD-TYPE 97 94 94

Figure S39.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S40.  Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
15Q LOSS MUTATED 65 74 141
15Q LOSS WILD-TYPE 106 132 61

Figure S40.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.011

Table S41.  Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
15Q LOSS MUTATED 114 69 94
15Q LOSS WILD-TYPE 58 106 127

Figure S41.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.16

Table S42.  Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
22Q LOSS MUTATED 120 139 171
22Q LOSS WILD-TYPE 51 67 31

Figure S42.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = OV-TP.transferedmergedcluster.txt

  • Number of patients = 579

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 14

  • 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)