Correlation between copy number variations of arm-level result and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13777G7
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 13 molecular subtypes across 569 patients, 34 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', and 'MRNASEQ_CNMF'.

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

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF'.

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

  • 12q gain cnv correlated to 'CN_CNMF'.

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

  • 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 'MRNA_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 5p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF'.

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

  • 17q loss cnv correlated to 'MIRSEQ_MATURE_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 13 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 34 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
MIR
CNMF
MIR
CHIERARCHICAL
CN
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
2p gain 178 (31%) 391 1e-05
(0.0104)
1e-05
(0.0104)
0.821
(1.00)
0.00042
(0.42)
1e-05
(0.0104)
0.0388
(1.00)
0.0942
(1.00)
0.00014
(0.142)
0.00158
(1.00)
0.823
(1.00)
0.0268
(1.00)
0.792
(1.00)
1
(1.00)
12p gain 250 (44%) 319 8e-05
(0.0814)
0.00076
(0.755)
0.742
(1.00)
0.0004
(0.4)
1e-05
(0.0104)
0.305
(1.00)
0.319
(1.00)
0.00038
(0.381)
0.00188
(1.00)
0.183
(1.00)
0.00023
(0.232)
0.303
(1.00)
0.11
(1.00)
20q gain 320 (56%) 249 1e-05
(0.0104)
0.00034
(0.342)
0.672
(1.00)
0.0001
(0.101)
1e-05
(0.0104)
0.662
(1.00)
0.0787
(1.00)
0.00889
(1.00)
0.136
(1.00)
0.258
(1.00)
0.00496
(1.00)
0.674
(1.00)
0.509
(1.00)
2q gain 150 (26%) 419 0.00044
(0.44)
5e-05
(0.051)
0.984
(1.00)
0.00491
(1.00)
1e-05
(0.0104)
0.0987
(1.00)
0.407
(1.00)
0.00371
(1.00)
0.0187
(1.00)
0.611
(1.00)
0.00614
(1.00)
0.105
(1.00)
0.726
(1.00)
13q gain 60 (11%) 509 0.00591
(1.00)
0.0002
(0.202)
0.574
(1.00)
0.0166
(1.00)
0.00016
(0.162)
0.593
(1.00)
0.317
(1.00)
0.231
(1.00)
0.43
(1.00)
0.192
(1.00)
0.0722
(1.00)
0.941
(1.00)
0.686
(1.00)
15q loss 276 (49%) 293 0.00051
(0.508)
0.0134
(1.00)
9e-05
(0.0914)
0.00036
(0.361)
1e-05
(0.0104)
0.375
(1.00)
0.814
(1.00)
0.0663
(1.00)
0.616
(1.00)
0.00662
(1.00)
0.00082
(0.812)
0.0299
(1.00)
0.00253
(1.00)
1q gain 218 (38%) 351 0.78
(1.00)
0.27
(1.00)
0.695
(1.00)
0.229
(1.00)
1e-05
(0.0104)
0.453
(1.00)
0.507
(1.00)
0.435
(1.00)
0.276
(1.00)
0.204
(1.00)
0.0984
(1.00)
0.116
(1.00)
0.176
(1.00)
3q gain 268 (47%) 301 0.975
(1.00)
0.806
(1.00)
0.257
(1.00)
0.429
(1.00)
2e-05
(0.0204)
0.594
(1.00)
0.256
(1.00)
0.696
(1.00)
0.926
(1.00)
0.181
(1.00)
0.0879
(1.00)
0.118
(1.00)
0.206
(1.00)
5p gain 196 (34%) 373 0.593
(1.00)
0.671
(1.00)
0.854
(1.00)
0.736
(1.00)
0.00012
(0.122)
0.485
(1.00)
0.0883
(1.00)
0.13
(1.00)
0.537
(1.00)
0.23
(1.00)
0.634
(1.00)
0.632
(1.00)
0.181
(1.00)
6p gain 166 (29%) 403 0.511
(1.00)
0.00438
(1.00)
0.901
(1.00)
0.0129
(1.00)
1e-05
(0.0104)
0.864
(1.00)
0.228
(1.00)
0.158
(1.00)
0.0079
(1.00)
0.361
(1.00)
0.065
(1.00)
0.436
(1.00)
0.864
(1.00)
6q gain 96 (17%) 473 0.655
(1.00)
0.0525
(1.00)
0.822
(1.00)
0.0202
(1.00)
1e-05
(0.0104)
0.788
(1.00)
0.997
(1.00)
0.00505
(1.00)
0.0222
(1.00)
0.194
(1.00)
0.0297
(1.00)
0.469
(1.00)
0.643
(1.00)
7p gain 181 (32%) 388 0.631
(1.00)
0.535
(1.00)
0.072
(1.00)
0.103
(1.00)
1e-05
(0.0104)
0.503
(1.00)
0.402
(1.00)
0.567
(1.00)
0.698
(1.00)
0.925
(1.00)
0.115
(1.00)
0.363
(1.00)
0.435
(1.00)
7q gain 198 (35%) 371 0.653
(1.00)
0.0847
(1.00)
0.297
(1.00)
0.379
(1.00)
2e-05
(0.0204)
0.463
(1.00)
0.247
(1.00)
0.925
(1.00)
0.643
(1.00)
0.153
(1.00)
0.633
(1.00)
0.0538
(1.00)
0.451
(1.00)
10p gain 184 (32%) 385 0.00397
(1.00)
0.021
(1.00)
0.679
(1.00)
0.376
(1.00)
1e-05
(0.0104)
0.979
(1.00)
0.0101
(1.00)
0.0111
(1.00)
0.124
(1.00)
0.56
(1.00)
0.00065
(0.646)
0.511
(1.00)
0.892
(1.00)
12q gain 174 (31%) 395 0.00601
(1.00)
0.0569
(1.00)
0.651
(1.00)
0.0486
(1.00)
1e-05
(0.0104)
0.0256
(1.00)
0.255
(1.00)
0.00185
(1.00)
0.00847
(1.00)
0.102
(1.00)
0.0111
(1.00)
0.581
(1.00)
0.101
(1.00)
19p gain 167 (29%) 402 0.0685
(1.00)
0.441
(1.00)
0.568
(1.00)
0.116
(1.00)
6e-05
(0.0611)
0.0555
(1.00)
0.21
(1.00)
0.235
(1.00)
0.471
(1.00)
0.369
(1.00)
0.334
(1.00)
0.544
(1.00)
0.981
(1.00)
19q gain 160 (28%) 409 0.208
(1.00)
0.768
(1.00)
0.861
(1.00)
0.184
(1.00)
1e-05
(0.0104)
0.494
(1.00)
0.38
(1.00)
0.206
(1.00)
0.437
(1.00)
0.272
(1.00)
0.677
(1.00)
0.434
(1.00)
0.991
(1.00)
20p gain 282 (50%) 287 0.00144
(1.00)
0.00106
(1.00)
0.725
(1.00)
0.00076
(0.755)
1e-05
(0.0104)
0.341
(1.00)
0.332
(1.00)
0.00267
(1.00)
0.123
(1.00)
0.224
(1.00)
0.00166
(1.00)
0.602
(1.00)
0.813
(1.00)
1p loss 61 (11%) 508 0.0297
(1.00)
0.00011
(0.112)
0.605
(1.00)
0.239
(1.00)
0.451
(1.00)
0.0351
(1.00)
0.203
(1.00)
0.632
(1.00)
0.509
(1.00)
0.447
(1.00)
0.306
(1.00)
0.0408
(1.00)
0.138
(1.00)
3p loss 95 (17%) 474 0.04
(1.00)
0.00094
(0.926)
0.889
(1.00)
0.0061
(1.00)
8e-05
(0.0814)
0.634
(1.00)
0.278
(1.00)
0.0623
(1.00)
0.00643
(1.00)
0.124
(1.00)
0.0921
(1.00)
0.921
(1.00)
0.743
(1.00)
5p loss 129 (23%) 440 0.0963
(1.00)
0.028
(1.00)
0.486
(1.00)
0.0833
(1.00)
0.0215
(1.00)
0.108
(1.00)
0.0775
(1.00)
0.00017
(0.172)
0.0481
(1.00)
0.665
(1.00)
0.0872
(1.00)
0.383
(1.00)
0.388
(1.00)
9q loss 280 (49%) 289 0.00488
(1.00)
0.0141
(1.00)
0.226
(1.00)
0.0247
(1.00)
1e-05
(0.0104)
0.594
(1.00)
0.585
(1.00)
0.00456
(1.00)
0.0515
(1.00)
0.187
(1.00)
0.0502
(1.00)
0.257
(1.00)
0.0887
(1.00)
14q loss 208 (37%) 361 0.212
(1.00)
0.165
(1.00)
0.968
(1.00)
0.492
(1.00)
1e-05
(0.0104)
0.98
(1.00)
0.61
(1.00)
0.00393
(1.00)
0.0466
(1.00)
0.801
(1.00)
0.32
(1.00)
0.975
(1.00)
0.772
(1.00)
17q loss 376 (66%) 193 0.0603
(1.00)
0.0211
(1.00)
0.0261
(1.00)
0.0103
(1.00)
0.969
(1.00)
0.434
(1.00)
0.335
(1.00)
0.492
(1.00)
0.0947
(1.00)
0.058
(1.00)
0.621
(1.00)
0.00013
(0.132)
0.121
(1.00)
1p gain 166 (29%) 403 0.106
(1.00)
0.325
(1.00)
0.119
(1.00)
0.685
(1.00)
0.00258
(1.00)
0.0924
(1.00)
0.308
(1.00)
0.612
(1.00)
0.949
(1.00)
0.215
(1.00)
0.618
(1.00)
0.151
(1.00)
0.339
(1.00)
3p gain 154 (27%) 415 0.339
(1.00)
0.389
(1.00)
0.0441
(1.00)
0.374
(1.00)
0.0126
(1.00)
1
(1.00)
0.406
(1.00)
0.783
(1.00)
0.766
(1.00)
0.918
(1.00)
0.821
(1.00)
0.906
(1.00)
1
(1.00)
4p gain 57 (10%) 512 0.246
(1.00)
0.19
(1.00)
0.00486
(1.00)
0.0595
(1.00)
0.134
(1.00)
0.456
(1.00)
0.397
(1.00)
0.606
(1.00)
0.841
(1.00)
0.32
(1.00)
0.0186
(1.00)
0.583
(1.00)
0.158
(1.00)
4q gain 32 (6%) 537 0.673
(1.00)
0.696
(1.00)
0.153
(1.00)
0.207
(1.00)
0.0371
(1.00)
0.27
(1.00)
0.45
(1.00)
0.764
(1.00)
0.856
(1.00)
0.374
(1.00)
0.0442
(1.00)
0.495
(1.00)
0.166
(1.00)
5q gain 60 (11%) 509 0.0834
(1.00)
0.244
(1.00)
0.802
(1.00)
0.832
(1.00)
0.51
(1.00)
0.441
(1.00)
0.389
(1.00)
0.709
(1.00)
0.413
(1.00)
0.496
(1.00)
0.81
(1.00)
0.629
(1.00)
0.311
(1.00)
8p gain 117 (21%) 452 0.0709
(1.00)
0.00363
(1.00)
0.299
(1.00)
0.362
(1.00)
0.715
(1.00)
0.136
(1.00)
0.00705
(1.00)
0.616
(1.00)
1
(1.00)
0.102
(1.00)
0.496
(1.00)
0.177
(1.00)
0.0663
(1.00)
8q gain 238 (42%) 331 0.02
(1.00)
0.00093
(0.917)
0.0614
(1.00)
0.2
(1.00)
0.175
(1.00)
0.32
(1.00)
0.387
(1.00)
0.0308
(1.00)
0.0862
(1.00)
0.464
(1.00)
0.865
(1.00)
0.293
(1.00)
0.379
(1.00)
9p gain 91 (16%) 478 0.113
(1.00)
0.424
(1.00)
0.238
(1.00)
0.866
(1.00)
0.019
(1.00)
0.395
(1.00)
0.727
(1.00)
0.693
(1.00)
0.412
(1.00)
0.186
(1.00)
0.186
(1.00)
0.496
(1.00)
0.329
(1.00)
9q gain 45 (8%) 524 0.252
(1.00)
0.303
(1.00)
0.0907
(1.00)
0.534
(1.00)
0.17
(1.00)
0.577
(1.00)
0.0266
(1.00)
0.486
(1.00)
0.09
(1.00)
0.499
(1.00)
0.754
(1.00)
0.474
(1.00)
0.503
(1.00)
10q gain 108 (19%) 461 0.00375
(1.00)
0.00919
(1.00)
0.242
(1.00)
0.118
(1.00)
0.0012
(1.00)
0.765
(1.00)
0.0622
(1.00)
0.105
(1.00)
0.22
(1.00)
0.728
(1.00)
0.244
(1.00)
0.96
(1.00)
0.294
(1.00)
11p gain 76 (13%) 493 0.711
(1.00)
0.1
(1.00)
0.64
(1.00)
0.468
(1.00)
0.343
(1.00)
0.0282
(1.00)
0.026
(1.00)
0.0592
(1.00)
0.0359
(1.00)
0.561
(1.00)
0.839
(1.00)
0.892
(1.00)
0.361
(1.00)
11q gain 114 (20%) 455 0.456
(1.00)
0.338
(1.00)
0.876
(1.00)
0.12
(1.00)
0.0394
(1.00)
0.165
(1.00)
0.00037
(0.371)
0.302
(1.00)
0.158
(1.00)
0.514
(1.00)
0.808
(1.00)
0.842
(1.00)
0.762
(1.00)
14q gain 58 (10%) 511 0.141
(1.00)
0.191
(1.00)
0.406
(1.00)
0.699
(1.00)
0.799
(1.00)
0.331
(1.00)
0.173
(1.00)
0.505
(1.00)
0.57
(1.00)
0.657
(1.00)
0.632
(1.00)
0.563
(1.00)
0.718
(1.00)
15q gain 39 (7%) 530 0.846
(1.00)
0.481
(1.00)
0.0852
(1.00)
0.755
(1.00)
0.419
(1.00)
0.114
(1.00)
0.108
(1.00)
0.735
(1.00)
0.933
(1.00)
0.316
(1.00)
0.2
(1.00)
0.526
(1.00)
0.109
(1.00)
16p gain 58 (10%) 511 0.00273
(1.00)
0.00482
(1.00)
0.402
(1.00)
0.177
(1.00)
0.089
(1.00)
0.343
(1.00)
0.0346
(1.00)
0.651
(1.00)
0.799
(1.00)
0.123
(1.00)
0.0808
(1.00)
0.197
(1.00)
0.0636
(1.00)
16q gain 30 (5%) 539 0.00087
(0.86)
0.0433
(1.00)
0.162
(1.00)
0.221
(1.00)
0.688
(1.00)
0.45
(1.00)
0.0266
(1.00)
1
(1.00)
0.361
(1.00)
0.00097
(0.954)
0.105
(1.00)
0.00249
(1.00)
0.00061
(0.607)
17p gain 22 (4%) 547 0.433
(1.00)
0.112
(1.00)
0.0561
(1.00)
0.0522
(1.00)
0.225
(1.00)
0.5
(1.00)
0.408
(1.00)
0.212
(1.00)
0.00336
(1.00)
0.175
(1.00)
0.837
(1.00)
0.411
(1.00)
0.67
(1.00)
17q gain 49 (9%) 520 0.322
(1.00)
0.0441
(1.00)
0.86
(1.00)
0.0487
(1.00)
0.791
(1.00)
0.448
(1.00)
0.277
(1.00)
0.937
(1.00)
0.0229
(1.00)
0.791
(1.00)
0.849
(1.00)
0.455
(1.00)
0.93
(1.00)
18p gain 117 (21%) 452 0.228
(1.00)
0.133
(1.00)
0.928
(1.00)
0.403
(1.00)
0.00512
(1.00)
0.0222
(1.00)
0.11
(1.00)
0.812
(1.00)
0.689
(1.00)
0.352
(1.00)
0.234
(1.00)
0.348
(1.00)
0.306
(1.00)
18q gain 71 (12%) 498 0.648
(1.00)
0.237
(1.00)
0.285
(1.00)
0.359
(1.00)
0.0518
(1.00)
0.513
(1.00)
0.398
(1.00)
0.486
(1.00)
0.271
(1.00)
0.108
(1.00)
0.196
(1.00)
0.055
(1.00)
0.102
(1.00)
21q gain 109 (19%) 460 0.29
(1.00)
0.881
(1.00)
0.961
(1.00)
0.582
(1.00)
0.00136
(1.00)
0.456
(1.00)
0.393
(1.00)
0.337
(1.00)
0.843
(1.00)
0.0237
(1.00)
0.0431
(1.00)
0.0991
(1.00)
0.763
(1.00)
22q gain 25 (4%) 544 0.565
(1.00)
0.585
(1.00)
0.901
(1.00)
0.634
(1.00)
0.126
(1.00)
0.366
(1.00)
0.262
(1.00)
0.464
(1.00)
0.529
(1.00)
0.0541
(1.00)
0.0548
(1.00)
0.0914
(1.00)
0.042
(1.00)
xq gain 104 (18%) 465 0.554
(1.00)
0.728
(1.00)
0.836
(1.00)
0.211
(1.00)
0.00236
(1.00)
0.276
(1.00)
0.791
(1.00)
0.797
(1.00)
0.822
(1.00)
0.552
(1.00)
0.364
(1.00)
0.476
(1.00)
0.541
(1.00)
1q loss 39 (7%) 530 0.0955
(1.00)
0.00814
(1.00)
0.121
(1.00)
0.704
(1.00)
0.978
(1.00)
0.352
(1.00)
0.523
(1.00)
0.466
(1.00)
1
(1.00)
0.97
(1.00)
0.934
(1.00)
0.24
(1.00)
0.71
(1.00)
2p loss 53 (9%) 516 0.932
(1.00)
0.0417
(1.00)
0.823
(1.00)
0.441
(1.00)
0.514
(1.00)
0.482
(1.00)
0.895
(1.00)
0.64
(1.00)
0.816
(1.00)
0.721
(1.00)
0.4
(1.00)
0.601
(1.00)
0.779
(1.00)
2q loss 59 (10%) 510 0.968
(1.00)
0.261
(1.00)
0.761
(1.00)
0.145
(1.00)
0.779
(1.00)
0.795
(1.00)
0.945
(1.00)
0.679
(1.00)
0.928
(1.00)
0.677
(1.00)
0.35
(1.00)
0.665
(1.00)
0.245
(1.00)
3q loss 41 (7%) 528 0.0206
(1.00)
0.0467
(1.00)
0.304
(1.00)
0.0546
(1.00)
0.00598
(1.00)
1
(1.00)
0.627
(1.00)
0.252
(1.00)
0.0768
(1.00)
0.223
(1.00)
0.00223
(1.00)
0.288
(1.00)
0.221
(1.00)
4p loss 312 (55%) 257 0.464
(1.00)
0.0276
(1.00)
0.282
(1.00)
0.521
(1.00)
0.00436
(1.00)
0.144
(1.00)
0.131
(1.00)
0.612
(1.00)
0.436
(1.00)
0.0667
(1.00)
0.13
(1.00)
0.0546
(1.00)
0.559
(1.00)
4q loss 355 (62%) 214 0.287
(1.00)
0.114
(1.00)
0.451
(1.00)
0.646
(1.00)
0.00155
(1.00)
0.101
(1.00)
0.016
(1.00)
0.356
(1.00)
0.351
(1.00)
0.14
(1.00)
0.113
(1.00)
0.0272
(1.00)
0.264
(1.00)
5q loss 218 (38%) 351 0.0005
(0.499)
0.0017
(1.00)
0.775
(1.00)
0.0136
(1.00)
0.00083
(0.821)
0.0458
(1.00)
0.117
(1.00)
0.0009
(0.888)
0.145
(1.00)
0.549
(1.00)
0.0106
(1.00)
0.301
(1.00)
0.128
(1.00)
6p loss 164 (29%) 405 0.962
(1.00)
0.0189
(1.00)
0.37
(1.00)
0.47
(1.00)
0.0594
(1.00)
0.701
(1.00)
0.896
(1.00)
0.412
(1.00)
0.0435
(1.00)
0.48
(1.00)
0.101
(1.00)
0.318
(1.00)
0.946
(1.00)
6q loss 239 (42%) 330 0.963
(1.00)
0.0771
(1.00)
0.435
(1.00)
0.0989
(1.00)
0.0178
(1.00)
0.625
(1.00)
0.653
(1.00)
0.0186
(1.00)
0.021
(1.00)
0.792
(1.00)
0.572
(1.00)
0.923
(1.00)
0.88
(1.00)
7p loss 118 (21%) 451 0.982
(1.00)
0.356
(1.00)
0.433
(1.00)
0.71
(1.00)
0.302
(1.00)
0.599
(1.00)
0.277
(1.00)
0.621
(1.00)
0.587
(1.00)
0.536
(1.00)
0.804
(1.00)
0.779
(1.00)
0.589
(1.00)
7q loss 81 (14%) 488 0.333
(1.00)
0.0863
(1.00)
0.348
(1.00)
0.301
(1.00)
0.92
(1.00)
0.821
(1.00)
0.0697
(1.00)
0.476
(1.00)
0.311
(1.00)
0.123
(1.00)
0.821
(1.00)
0.503
(1.00)
0.416
(1.00)
8p loss 271 (48%) 298 0.741
(1.00)
0.892
(1.00)
0.241
(1.00)
0.946
(1.00)
0.00357
(1.00)
0.118
(1.00)
0.301
(1.00)
0.483
(1.00)
0.705
(1.00)
0.701
(1.00)
0.0376
(1.00)
0.81
(1.00)
0.405
(1.00)
8q loss 88 (15%) 481 0.00809
(1.00)
0.00479
(1.00)
0.522
(1.00)
0.263
(1.00)
0.00185
(1.00)
0.0215
(1.00)
0.233
(1.00)
0.00094
(0.926)
0.028
(1.00)
0.662
(1.00)
0.124
(1.00)
0.76
(1.00)
0.398
(1.00)
9p loss 255 (45%) 314 0.00321
(1.00)
0.00637
(1.00)
0.512
(1.00)
0.186
(1.00)
0.00812
(1.00)
0.791
(1.00)
0.544
(1.00)
0.898
(1.00)
0.108
(1.00)
0.0541
(1.00)
0.256
(1.00)
0.0638
(1.00)
0.0378
(1.00)
10p loss 94 (17%) 475 0.296
(1.00)
1
(1.00)
0.262
(1.00)
0.369
(1.00)
0.562
(1.00)
0.602
(1.00)
0.0604
(1.00)
0.814
(1.00)
0.638
(1.00)
0.45
(1.00)
0.812
(1.00)
0.423
(1.00)
0.252
(1.00)
10q loss 122 (21%) 447 0.973
(1.00)
0.86
(1.00)
0.00395
(1.00)
0.328
(1.00)
0.0815
(1.00)
0.365
(1.00)
0.371
(1.00)
0.662
(1.00)
0.724
(1.00)
0.766
(1.00)
0.347
(1.00)
0.87
(1.00)
0.0592
(1.00)
11p loss 193 (34%) 376 0.239
(1.00)
0.0115
(1.00)
0.546
(1.00)
0.309
(1.00)
0.124
(1.00)
0.0982
(1.00)
0.612
(1.00)
0.0405
(1.00)
0.112
(1.00)
0.473
(1.00)
0.143
(1.00)
0.0772
(1.00)
0.097
(1.00)
11q loss 144 (25%) 425 0.356
(1.00)
0.8
(1.00)
0.179
(1.00)
0.538
(1.00)
0.0155
(1.00)
0.462
(1.00)
0.71
(1.00)
0.271
(1.00)
0.798
(1.00)
0.514
(1.00)
0.215
(1.00)
0.102
(1.00)
0.27
(1.00)
12p loss 78 (14%) 491 0.003
(1.00)
0.0108
(1.00)
0.539
(1.00)
0.0103
(1.00)
0.00297
(1.00)
0.783
(1.00)
0.133
(1.00)
0.313
(1.00)
0.205
(1.00)
0.00938
(1.00)
0.00637
(1.00)
0.00225
(1.00)
0.0171
(1.00)
12q loss 104 (18%) 465 0.0682
(1.00)
0.0793
(1.00)
0.759
(1.00)
0.233
(1.00)
0.0587
(1.00)
0.268
(1.00)
0.557
(1.00)
0.244
(1.00)
0.196
(1.00)
0.0431
(1.00)
0.0484
(1.00)
0.111
(1.00)
0.081
(1.00)
13q loss 303 (53%) 266 0.0346
(1.00)
0.00675
(1.00)
0.791
(1.00)
0.013
(1.00)
0.00584
(1.00)
0.0104
(1.00)
0.395
(1.00)
0.466
(1.00)
0.418
(1.00)
0.254
(1.00)
0.504
(1.00)
0.096
(1.00)
0.168
(1.00)
16p loss 325 (57%) 244 0.321
(1.00)
0.827
(1.00)
0.0375
(1.00)
0.318
(1.00)
0.124
(1.00)
0.804
(1.00)
0.201
(1.00)
0.0522
(1.00)
0.309
(1.00)
0.0791
(1.00)
0.0814
(1.00)
0.112
(1.00)
0.199
(1.00)
16q loss 404 (71%) 165 0.567
(1.00)
0.857
(1.00)
0.00361
(1.00)
0.0974
(1.00)
0.00174
(1.00)
0.948
(1.00)
0.245
(1.00)
0.204
(1.00)
0.426
(1.00)
0.0726
(1.00)
0.156
(1.00)
0.0479
(1.00)
0.175
(1.00)
17p loss 471 (83%) 98 0.277
(1.00)
0.216
(1.00)
0.18
(1.00)
0.17
(1.00)
0.482
(1.00)
0.55
(1.00)
0.24
(1.00)
0.101
(1.00)
0.058
(1.00)
0.47
(1.00)
0.476
(1.00)
0.137
(1.00)
0.419
(1.00)
18p loss 234 (41%) 335 0.416
(1.00)
0.894
(1.00)
0.509
(1.00)
0.0224
(1.00)
0.235
(1.00)
0.312
(1.00)
0.00629
(1.00)
0.0231
(1.00)
0.113
(1.00)
0.837
(1.00)
0.541
(1.00)
0.61
(1.00)
0.776
(1.00)
18q loss 290 (51%) 279 0.316
(1.00)
0.878
(1.00)
0.407
(1.00)
0.978
(1.00)
0.971
(1.00)
0.812
(1.00)
0.0478
(1.00)
0.0113
(1.00)
0.0898
(1.00)
0.977
(1.00)
0.779
(1.00)
0.822
(1.00)
0.787
(1.00)
19p loss 181 (32%) 388 0.986
(1.00)
0.44
(1.00)
0.236
(1.00)
0.0228
(1.00)
0.017
(1.00)
0.0208
(1.00)
0.859
(1.00)
0.745
(1.00)
0.255
(1.00)
0.8
(1.00)
0.106
(1.00)
0.861
(1.00)
0.601
(1.00)
19q loss 172 (30%) 397 0.823
(1.00)
0.39
(1.00)
0.284
(1.00)
0.0153
(1.00)
0.0386
(1.00)
0.091
(1.00)
0.617
(1.00)
1
(1.00)
0.483
(1.00)
0.363
(1.00)
0.0901
(1.00)
0.418
(1.00)
0.797
(1.00)
20p loss 49 (9%) 520 0.498
(1.00)
0.833
(1.00)
0.221
(1.00)
0.686
(1.00)
0.128
(1.00)
0.102
(1.00)
0.2
(1.00)
0.012
(1.00)
0.00055
(0.548)
0.0008
(0.793)
0.173
(1.00)
0.00631
(1.00)
0.485
(1.00)
20q loss 31 (5%) 538 0.115
(1.00)
0.498
(1.00)
0.0382
(1.00)
0.505
(1.00)
0.512
(1.00)
0.0484
(1.00)
0.097
(1.00)
0.132
(1.00)
0.0136
(1.00)
0.136
(1.00)
0.378
(1.00)
0.0648
(1.00)
0.202
(1.00)
21q loss 195 (34%) 374 0.82
(1.00)
0.0532
(1.00)
0.386
(1.00)
0.179
(1.00)
0.397
(1.00)
0.651
(1.00)
0.438
(1.00)
0.585
(1.00)
0.408
(1.00)
0.688
(1.00)
0.729
(1.00)
0.144
(1.00)
0.422
(1.00)
22q loss 421 (74%) 148 0.00517
(1.00)
0.0929
(1.00)
0.0359
(1.00)
0.136
(1.00)
0.00034
(0.342)
0.0705
(1.00)
0.00953
(1.00)
0.191
(1.00)
0.129
(1.00)
0.0425
(1.00)
0.609
(1.00)
0.0496
(1.00)
0.0237
(1.00)
xq loss 273 (48%) 296 0.0588
(1.00)
0.164
(1.00)
0.289
(1.00)
0.87
(1.00)
0.00584
(1.00)
0.387
(1.00)
0.0453
(1.00)
0.495
(1.00)
0.898
(1.00)
0.799
(1.00)
0.402
(1.00)
0.896
(1.00)
0.159
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
1Q GAIN MUTATED 58 57 103
1Q GAIN WILD-TYPE 116 149 86

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 = 0.01

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 44 36
2P GAIN WILD-TYPE 122 172 90

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

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 76 48 49
2P GAIN WILD-TYPE 234 110 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 = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
2P GAIN MUTATED 35 47 96
2P GAIN WILD-TYPE 139 159 93

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.14

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #8: '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 S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.051

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2Q GAIN MUTATED 69 36 41
2Q GAIN WILD-TYPE 241 122 48

Figure S6.  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 = 0.01

Table S7.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
2Q GAIN MUTATED 29 40 81
2Q GAIN WILD-TYPE 145 166 108

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.02

Table S8.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
3Q GAIN MUTATED 63 89 116
3Q GAIN WILD-TYPE 111 117 73

Figure S8.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
5P GAIN MUTATED 38 78 80
5P GAIN WILD-TYPE 136 128 109

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

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S10.  Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
6P GAIN MUTATED 30 57 79
6P GAIN WILD-TYPE 144 149 110

Figure S10.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S11.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
6Q GAIN MUTATED 12 31 53
6Q GAIN WILD-TYPE 162 175 136

Figure S11.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
7P GAIN MUTATED 46 47 88
7P GAIN WILD-TYPE 128 159 101

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.02

Table S13.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
7Q GAIN MUTATED 47 60 91
7Q GAIN WILD-TYPE 127 146 98

Figure S13.  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 = 0.01

Table S14.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
10P GAIN MUTATED 39 48 97
10P GAIN WILD-TYPE 135 158 92

Figure S14.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.081

Table S15.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
12P GAIN MUTATED 119 75 49
12P GAIN WILD-TYPE 96 141 77

Figure S15.  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 = 0.01

Table S16.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
12P GAIN MUTATED 55 69 126
12P GAIN WILD-TYPE 119 137 63

Figure S16.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.23

Table S17.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12P GAIN MUTATED 27 39 81 46
12P GAIN WILD-TYPE 78 32 84 60

Figure S17.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S18.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
12Q GAIN MUTATED 40 38 96
12Q GAIN WILD-TYPE 134 168 93

Figure S18.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.2

Table S19.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
13Q GAIN MUTATED 19 20 19
13Q GAIN WILD-TYPE 291 138 70

Figure S19.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
13Q GAIN MUTATED 22 8 30
13Q GAIN WILD-TYPE 152 198 159

Figure S20.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.061

Table S21.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
19P GAIN MUTATED 34 56 77
19P GAIN WILD-TYPE 140 150 112

Figure S21.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S22.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
19Q GAIN MUTATED 33 49 78
19Q GAIN WILD-TYPE 141 157 111

Figure S22.  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 = 0.01

Table S23.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
20P GAIN MUTATED 64 85 133
20P GAIN WILD-TYPE 110 121 56

Figure S23.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S24.  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 S24.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.1

Table S25.  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 S25.  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 = 0.01

Table S26.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
20Q GAIN MUTATED 68 103 149
20Q GAIN WILD-TYPE 106 103 40

Figure S26.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.11

Table S27.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
1P LOSS MUTATED 30 9 21
1P LOSS WILD-TYPE 280 149 68

Figure S27.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.081

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
3P LOSS MUTATED 21 24 50
3P LOSS WILD-TYPE 153 182 139

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

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #49: '5p loss' versus Molecular Subtype #8: '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 S29.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S30.  Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
9Q LOSS MUTATED 81 68 131
9Q LOSS WILD-TYPE 93 138 58

Figure S30.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S31.  Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
14Q LOSS MUTATED 52 61 95
14Q LOSS WILD-TYPE 122 145 94

Figure S31.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'MIR_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.091

Table S32.  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 70 137
15Q LOSS WILD-TYPE 97 94 95

Figure S32.  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 = 0.01

Table S33.  Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
15Q LOSS MUTATED 66 78 132
15Q LOSS WILD-TYPE 108 128 57

Figure S33.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.13

Table S34.  Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 195 157
17Q LOSS MUTATED 46 145 107
17Q LOSS WILD-TYPE 49 50 50

Figure S34.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CNMF'

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

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

  • Number of patients = 569

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 13

  • 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)