Correlation between copy number variation genes (focal events) and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1XS5SV0
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5SV0
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 14 molecular subtypes across 569 patients, 43 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q cnv correlated to 'CN_CNMF'.

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

  • 2q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3p cnv correlated to 'CN_CNMF'.

  • 3q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 5p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 5q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7p cnv correlated to 'CN_CNMF'.

  • 7q cnv correlated to 'CN_CNMF'.

  • 9p cnv correlated to 'CN_CNMF'.

  • 9q cnv correlated to 'CN_CNMF'.

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

  • 10q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q cnv correlated to 'CN_CNMF'.

  • 12p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12q cnv correlated to 'CN_CNMF'.

  • 14q cnv correlated to 'CN_CNMF'.

  • 15q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 16q cnv correlated to 'CN_CNMF'.

  • 17q cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 19p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

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

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

  • 21q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal 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, 43 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 Chi-square 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 231 (41%) 338 1.4e-05
(0.0075) 		3e-05
(0.016) 		0.622
(1.00) 		0.00192
(0.965) 		1.14e-08
(6.28e-06) 		5.37e-07
(0.000292) 		0.0309
(1.00) 		0.494
(1.00) 		0.0023
(1.00) 		0.0713
(1.00) 		0.876
(1.00) 		0.883
(1.00) 		0.423
(1.00) 		0.303
(1.00)
15q 315 (55%) 254 0.00037
(0.192) 		0.00022
(0.114) 		0.00155
(0.783) 		0.0061
(1.00) 		8.21e-11
(4.59e-08) 		4.43e-06
(0.0024) 		0.2
(1.00) 		0.508
(1.00) 		0.0369
(1.00) 		0.541
(1.00) 		0.0137
(1.00) 		0.555
(1.00) 		0.0435
(1.00) 		0.0113
(1.00)
20q 351 (62%) 218 0.00028
(0.145) 		0.00466
(1.00) 		0.604
(1.00) 		0.00207
(1.00) 		3.71e-14
(2.07e-11) 		1.6e-09
(8.87e-07) 		0.135
(1.00) 		0.24
(1.00) 		0.00683
(1.00) 		0.879
(1.00) 		0.455
(1.00) 		0.873
(1.00) 		0.921
(1.00) 		0.775
(1.00)
2q 209 (37%) 360 0.00159
(0.801) 		0.00123
(0.627) 		0.854
(1.00) 		0.0285
(1.00) 		2.68e-07
(0.000147) 		0.000147
(0.0773) 		0.0525
(1.00) 		0.469
(1.00) 		0.0365
(1.00) 		0.26
(1.00) 		0.78
(1.00) 		0.877
(1.00) 		0.196
(1.00) 		0.569
(1.00)
3q 309 (54%) 260 0.256
(1.00) 		0.0843
(1.00) 		0.61
(1.00) 		0.106
(1.00) 		2.28e-10
(1.27e-07) 		2.88e-05
(0.0154) 		0.576
(1.00) 		0.428
(1.00) 		0.249
(1.00) 		0.443
(1.00) 		0.178
(1.00) 		0.28
(1.00) 		0.467
(1.00) 		0.312
(1.00)
5p 325 (57%) 244 0.23
(1.00) 		0.226
(1.00) 		0.745
(1.00) 		0.0971
(1.00) 		4.47e-08
(2.46e-05) 		5.35e-05
(0.0284) 		0.0704
(1.00) 		0.304
(1.00) 		0.103
(1.00) 		0.621
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.174
(1.00) 		0.95
(1.00)
5q 278 (49%) 291 0.017
(1.00) 		0.142
(1.00) 		0.713
(1.00) 		0.0085
(1.00) 		5.91e-05
(0.0312) 		5.69e-06
(0.00307) 		0.0205
(1.00) 		0.142
(1.00) 		0.00305
(1.00) 		0.82
(1.00) 		0.205
(1.00) 		0.2
(1.00) 		0.122
(1.00) 		0.379
(1.00)
10p 278 (49%) 291 0.0374
(1.00) 		0.066
(1.00) 		0.15
(1.00) 		0.0277
(1.00) 		3.73e-09
(2.07e-06) 		2.02e-06
(0.00109) 		0.607
(1.00) 		0.949
(1.00) 		0.0272
(1.00) 		0.169
(1.00) 		0.664
(1.00) 		0.932
(1.00) 		0.82
(1.00) 		0.218
(1.00)
10q 230 (40%) 339 0.044
(1.00) 		0.0362
(1.00) 		0.0479
(1.00) 		0.00265
(1.00) 		8.95e-06
(0.00482) 		1.45e-05
(0.00777) 		0.214
(1.00) 		0.191
(1.00) 		0.0547
(1.00) 		0.0372
(1.00) 		0.45
(1.00) 		0.724
(1.00) 		0.78
(1.00) 		0.605
(1.00)
12p 328 (58%) 241 0.00916
(1.00) 		0.0227
(1.00) 		0.974
(1.00) 		0.145
(1.00) 		4.53e-08
(2.48e-05) 		3.68e-05
(0.0196) 		0.345
(1.00) 		0.76
(1.00) 		0.00963
(1.00) 		0.0546
(1.00) 		0.916
(1.00) 		0.427
(1.00) 		0.635
(1.00) 		0.959
(1.00)
19p 348 (61%) 221 0.123
(1.00) 		0.0994
(1.00) 		0.0867
(1.00) 		0.702
(1.00) 		9.98e-10
(5.55e-07) 		2.15e-05
(0.0115) 		0.353
(1.00) 		0.339
(1.00) 		0.073
(1.00) 		0.273
(1.00) 		0.74
(1.00) 		0.221
(1.00) 		0.762
(1.00) 		0.867
(1.00)
20p 331 (58%) 238 0.0114
(1.00) 		0.00792
(1.00) 		0.379
(1.00) 		0.000622
(0.32) 		7.04e-09
(3.9e-06) 		1.59e-06
(0.000862) 		0.0492
(1.00) 		0.231
(1.00) 		0.000912
(0.468) 		0.977
(1.00) 		0.641
(1.00) 		0.938
(1.00) 		0.734
(1.00) 		0.636
(1.00)
21q 304 (53%) 265 0.609
(1.00) 		0.265
(1.00) 		0.33
(1.00) 		0.529
(1.00) 		0.000158
(0.0827) 		0.000149
(0.0784) 		0.497
(1.00) 		0.359
(1.00) 		0.502
(1.00) 		0.413
(1.00) 		0.285
(1.00) 		0.537
(1.00) 		0.775
(1.00) 		0.608
(1.00)
1q 257 (45%) 312 0.292
(1.00) 		0.154
(1.00) 		0.603
(1.00) 		0.036
(1.00) 		2e-07
(0.000109) 		0.0039
(1.00) 		0.909
(1.00) 		0.969
(1.00) 		0.339
(1.00) 		0.642
(1.00) 		0.226
(1.00) 		0.427
(1.00) 		0.356
(1.00) 		0.304
(1.00)
3p 249 (44%) 320 0.371
(1.00) 		0.191
(1.00) 		0.175
(1.00) 		0.783
(1.00) 		1.87e-08
(1.03e-05) 		0.0123
(1.00) 		0.759
(1.00) 		0.395
(1.00) 		0.232
(1.00) 		0.713
(1.00) 		0.25
(1.00) 		0.538
(1.00) 		0.844
(1.00) 		0.443
(1.00)
7p 299 (53%) 270 0.636
(1.00) 		0.466
(1.00) 		0.565
(1.00) 		0.455
(1.00) 		5.25e-05
(0.0279) 		0.00149
(0.753) 		0.159
(1.00) 		0.863
(1.00) 		0.315
(1.00) 		0.461
(1.00) 		0.815
(1.00) 		0.934
(1.00) 		0.622
(1.00) 		0.765
(1.00)
7q 279 (49%) 290 0.708
(1.00) 		0.708
(1.00) 		0.883
(1.00) 		0.755
(1.00) 		6.58e-05
(0.0347) 		0.00998
(1.00) 		0.573
(1.00) 		0.617
(1.00) 		0.392
(1.00) 		0.702
(1.00) 		0.633
(1.00) 		0.733
(1.00) 		0.284
(1.00) 		0.82
(1.00)
9p 346 (61%) 223 0.185
(1.00) 		0.0968
(1.00) 		0.702
(1.00) 		0.373
(1.00) 		7.09e-06
(0.00382) 		0.0447
(1.00) 		0.922
(1.00) 		0.668
(1.00) 		0.635
(1.00) 		0.603
(1.00) 		0.488
(1.00) 		0.525
(1.00) 		0.295
(1.00) 		0.866
(1.00)
9q 325 (57%) 244 0.0357
(1.00) 		0.146
(1.00) 		0.563
(1.00) 		0.0868
(1.00) 		8.35e-11
(4.66e-08) 		0.0242
(1.00) 		0.339
(1.00) 		0.716
(1.00) 		0.00775
(1.00) 		0.392
(1.00) 		0.461
(1.00) 		0.365
(1.00) 		0.443
(1.00) 		0.239
(1.00)
11q 258 (45%) 311 0.67
(1.00) 		0.535
(1.00) 		0.469
(1.00) 		0.282
(1.00) 		0.000186
(0.0968) 		0.00124
(0.63) 		0.053
(1.00) 		0.509
(1.00) 		0.802
(1.00) 		0.52
(1.00) 		0.418
(1.00) 		0.397
(1.00) 		0.109
(1.00) 		0.385
(1.00)
12q 278 (49%) 291 0.438
(1.00) 		0.241
(1.00) 		0.865
(1.00) 		0.887
(1.00) 		2.84e-07
(0.000155) 		0.00497
(1.00) 		0.34
(1.00) 		0.719
(1.00) 		0.0645
(1.00) 		0.509
(1.00) 		0.723
(1.00) 		0.262
(1.00) 		0.724
(1.00) 		0.831
(1.00)
14q 266 (47%) 303 0.0273
(1.00) 		0.0381
(1.00) 		0.623
(1.00) 		0.209
(1.00) 		0.000137
(0.0723) 		0.000942
(0.482) 		0.572
(1.00) 		0.253
(1.00) 		0.0105
(1.00) 		0.0235
(1.00) 		0.491
(1.00) 		0.604
(1.00) 		0.708
(1.00) 		0.547
(1.00)
16q 434 (76%) 135 0.671
(1.00) 		0.302
(1.00) 		0.0157
(1.00) 		0.161
(1.00) 		0.000166
(0.0867) 		0.0338
(1.00) 		0.573
(1.00) 		0.985
(1.00) 		0.126
(1.00) 		0.727
(1.00) 		0.0954
(1.00) 		0.436
(1.00) 		0.0895
(1.00) 		0.868
(1.00)
17q 425 (75%) 144 0.262
(1.00) 		0.203
(1.00) 		0.0104
(1.00) 		0.573
(1.00) 		0.775
(1.00) 		0.399
(1.00) 		0.81
(1.00) 		0.661
(1.00) 		0.272
(1.00) 		0.538
(1.00) 		0.062
(1.00) 		0.133
(1.00) 		0.000439
(0.227) 		0.617
(1.00)
19q 332 (58%) 237 0.0967
(1.00) 		0.0599
(1.00) 		0.136
(1.00) 		0.737
(1.00) 		6.71e-08
(3.68e-05) 		0.000503
(0.26) 		0.475
(1.00) 		0.234
(1.00) 		0.236
(1.00) 		0.103
(1.00) 		0.96
(1.00) 		0.731
(1.00) 		0.988
(1.00) 		0.697
(1.00)
1p 227 (40%) 342 0.951
(1.00) 		0.928
(1.00) 		0.231
(1.00) 		0.0918
(1.00) 		0.0177
(1.00) 		0.144
(1.00) 		0.963
(1.00) 		0.998
(1.00) 		0.35
(1.00) 		0.771
(1.00) 		0.312
(1.00) 		0.873
(1.00) 		0.871
(1.00) 		0.668
(1.00)
4p 369 (65%) 200 0.233
(1.00) 		0.138
(1.00) 		0.562
(1.00) 		0.016
(1.00) 		0.00119
(0.608) 		0.0575
(1.00) 		0.0749
(1.00) 		0.0902
(1.00) 		0.219
(1.00) 		0.909
(1.00) 		0.336
(1.00) 		0.273
(1.00) 		0.176
(1.00) 		0.242
(1.00)
4q 387 (68%) 182 0.136
(1.00) 		0.125
(1.00) 		0.464
(1.00) 		0.0294
(1.00) 		0.0016
(0.805) 		0.0544
(1.00) 		0.0747
(1.00) 		0.0601
(1.00) 		0.382
(1.00) 		0.352
(1.00) 		0.389
(1.00) 		0.0888
(1.00) 		0.0565
(1.00) 		0.0242
(1.00)
6p 330 (58%) 239 0.69
(1.00) 		0.713
(1.00) 		0.654
(1.00) 		0.499
(1.00) 		0.0265
(1.00) 		0.0804
(1.00) 		0.569
(1.00) 		0.0485
(1.00) 		0.811
(1.00) 		0.908
(1.00) 		0.947
(1.00) 		0.737
(1.00) 		0.965
(1.00) 		0.829
(1.00)
6q 335 (59%) 234 0.702
(1.00) 		0.512
(1.00) 		0.72
(1.00) 		0.818
(1.00) 		0.35
(1.00) 		0.322
(1.00) 		0.327
(1.00) 		0.078
(1.00) 		0.665
(1.00) 		0.448
(1.00) 		0.724
(1.00) 		0.713
(1.00) 		0.848
(1.00) 		0.892
(1.00)
8p 388 (68%) 181 0.0292
(1.00) 		0.0125
(1.00) 		0.132
(1.00) 		0.0359
(1.00) 		0.000596
(0.307) 		0.22
(1.00) 		0.868
(1.00) 		0.6
(1.00) 		0.363
(1.00) 		0.826
(1.00) 		0.156
(1.00) 		0.313
(1.00) 		0.485
(1.00) 		0.0776
(1.00)
8q 326 (57%) 243 0.0452
(1.00) 		0.00464
(1.00) 		0.241
(1.00) 		0.0273
(1.00) 		0.0134
(1.00) 		0.00564
(1.00) 		0.687
(1.00) 		0.883
(1.00) 		0.922
(1.00) 		0.716
(1.00) 		0.41
(1.00) 		0.948
(1.00) 		0.356
(1.00) 		0.812
(1.00)
11p 269 (47%) 300 0.506
(1.00) 		0.209
(1.00) 		0.515
(1.00) 		0.323
(1.00) 		0.0215
(1.00) 		0.00225
(1.00) 		0.304
(1.00) 		0.821
(1.00) 		0.0935
(1.00) 		0.149
(1.00) 		0.257
(1.00) 		0.128
(1.00) 		0.0458
(1.00) 		0.16
(1.00)
13q 363 (64%) 206 0.7
(1.00) 		0.429
(1.00) 		0.705
(1.00) 		0.552
(1.00) 		0.048
(1.00) 		0.000962
(0.491) 		0.0372
(1.00) 		0.036
(1.00) 		0.41
(1.00) 		0.787
(1.00) 		0.848
(1.00) 		0.511
(1.00) 		0.0901
(1.00) 		0.904
(1.00)
16p 383 (67%) 186 0.159
(1.00) 		0.504
(1.00) 		0.132
(1.00) 		0.38
(1.00) 		0.00126
(0.638) 		0.00608
(1.00) 		0.949
(1.00) 		0.583
(1.00) 		0.0468
(1.00) 		0.675
(1.00) 		0.0953
(1.00) 		0.705
(1.00) 		0.2
(1.00) 		0.0918
(1.00)
17p 493 (87%) 76 0.528
(1.00) 		0.237
(1.00) 		0.626
(1.00) 		0.808
(1.00) 		0.112
(1.00) 		0.442
(1.00) 		0.867
(1.00) 		0.417
(1.00) 		0.4
(1.00) 		0.289
(1.00) 		0.189
(1.00) 		0.38
(1.00) 		0.0185
(1.00) 		0.546
(1.00)
18p 351 (62%) 218 0.392
(1.00) 		0.326
(1.00) 		0.453
(1.00) 		0.801
(1.00) 		0.0346
(1.00) 		0.0278
(1.00) 		0.411
(1.00) 		0.0439
(1.00) 		0.00474
(1.00) 		0.567
(1.00) 		0.355
(1.00) 		0.405
(1.00) 		0.523
(1.00) 		0.565
(1.00)
18q 361 (63%) 208 0.426
(1.00) 		0.117
(1.00) 		0.897
(1.00) 		0.924
(1.00) 		0.335
(1.00) 		0.122
(1.00) 		0.658
(1.00) 		0.011
(1.00) 		0.0168
(1.00) 		0.849
(1.00) 		0.341
(1.00) 		0.565
(1.00) 		0.0718
(1.00) 		0.572
(1.00)
22q 446 (78%) 123 0.0103
(1.00) 		0.0297
(1.00) 		0.0139
(1.00) 		0.0577
(1.00) 		0.000584
(0.301) 		0.0227
(1.00) 		0.196
(1.00) 		0.192
(1.00) 		0.0366
(1.00) 		0.859
(1.00) 		0.133
(1.00) 		0.24
(1.00) 		0.0521
(1.00) 		0.18
(1.00)
xq 377 (66%) 192 0.0197
(1.00) 		0.19
(1.00) 		0.127
(1.00) 		0.448
(1.00) 		0.0649
(1.00) 		0.11
(1.00) 		0.0229
(1.00) 		0.0204
(1.00) 		0.812
(1.00) 		0.474
(1.00) 		0.4
(1.00) 		0.586
(1.00) 		0.307
(1.00) 		0.493
(1.00)
'1q' versus 'CN_CNMF'

P value = 2e-07 (Fisher's exact test), Q value = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
1Q MUTATED 69 72 116
1Q WILD-TYPE 105 134 73

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

'2p' versus 'MRNA_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.0075

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
2P MUTATED 113 66 47
2P WILD-TYPE 102 150 79

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

'2p' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
2P MUTATED 48 110 68
2P WILD-TYPE 80 100 151

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

'2p' versus 'CN_CNMF'

P value = 1.14e-08 (Fisher's exact test), Q value = 6.3e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
2P MUTATED 52 69 110
2P WILD-TYPE 122 137 79

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

'2p' versus 'METHLYATION_CNMF'

P value = 5.37e-07 (Fisher's exact test), Q value = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2P MUTATED 99 57 75
2P WILD-TYPE 73 118 146

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

'2q' versus 'CN_CNMF'

P value = 2.68e-07 (Fisher's exact test), Q value = 0.00015

Table S6.  Gene #4: '2q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
2Q MUTATED 46 64 99
2Q WILD-TYPE 128 142 90

Figure S6.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #5: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.077

Table S7.  Gene #4: '2q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2Q MUTATED 85 50 74
2Q WILD-TYPE 87 125 147

Figure S7.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3p' versus 'CN_CNMF'

P value = 1.87e-08 (Fisher's exact test), Q value = 1e-05

Table S8.  Gene #5: '3p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
3P MUTATED 60 73 116
3P WILD-TYPE 114 133 73

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

'3q' versus 'CN_CNMF'

P value = 2.28e-10 (Fisher's exact test), Q value = 1.3e-07

Table S9.  Gene #6: '3q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
3Q MUTATED 73 97 139
3Q WILD-TYPE 101 109 50

Figure S9.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #5: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.015

Table S10.  Gene #6: '3q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
3Q MUTATED 118 85 105
3Q WILD-TYPE 54 90 116

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

'5p' versus 'CN_CNMF'

P value = 4.47e-08 (Fisher's exact test), Q value = 2.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
5P MUTATED 73 116 136
5P WILD-TYPE 101 90 53

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

'5p' versus 'METHLYATION_CNMF'

P value = 5.35e-05 (Fisher's exact test), Q value = 0.028

Table S12.  Gene #9: '5p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
5P MUTATED 119 80 126
5P WILD-TYPE 53 95 95

Figure S12.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q' versus 'CN_CNMF'

P value = 5.91e-05 (Fisher's exact test), Q value = 0.031

Table S13.  Gene #10: '5q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
5Q MUTATED 72 89 117
5Q WILD-TYPE 102 117 72

Figure S13.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #5: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 5.69e-06 (Fisher's exact test), Q value = 0.0031

Table S14.  Gene #10: '5q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
5Q MUTATED 111 73 94
5Q WILD-TYPE 61 102 127

Figure S14.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p' versus 'CN_CNMF'

P value = 5.25e-05 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
7P MUTATED 78 97 124
7P WILD-TYPE 96 109 65

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

'7q' versus 'CN_CNMF'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
7Q MUTATED 71 91 117
7Q WILD-TYPE 103 115 72

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

'9p' versus 'CN_CNMF'

P value = 7.09e-06 (Fisher's exact test), Q value = 0.0038

Table S17.  Gene #17: '9p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
9P MUTATED 97 108 141
9P WILD-TYPE 77 98 48

Figure S17.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #5: 'CN_CNMF'

'9q' versus 'CN_CNMF'

P value = 8.35e-11 (Fisher's exact test), Q value = 4.7e-08

Table S18.  Gene #18: '9q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
9Q MUTATED 91 90 144
9Q WILD-TYPE 83 116 45

Figure S18.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #5: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 3.73e-09 (Fisher's exact test), Q value = 2.1e-06

Table S19.  Gene #19: '10p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
10P MUTATED 72 79 127
10P WILD-TYPE 102 127 62

Figure S19.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0011

Table S20.  Gene #19: '10p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
10P MUTATED 112 71 95
10P WILD-TYPE 60 104 126

Figure S20.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q' versus 'CN_CNMF'

P value = 8.95e-06 (Fisher's exact test), Q value = 0.0048

Table S21.  Gene #20: '10q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
10Q MUTATED 56 71 103
10Q WILD-TYPE 118 135 86

Figure S21.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0078

Table S22.  Gene #20: '10q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
10Q MUTATED 95 57 78
10Q WILD-TYPE 77 118 143

Figure S22.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q' versus 'CN_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.097

Table S23.  Gene #22: '11q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
11Q MUTATED 60 92 106
11Q WILD-TYPE 114 114 83

Figure S23.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #5: 'CN_CNMF'

'12p' versus 'CN_CNMF'

P value = 4.53e-08 (Fisher's exact test), Q value = 2.5e-05

Table S24.  Gene #23: '12p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
12P MUTATED 80 108 140
12P WILD-TYPE 94 98 49

Figure S24.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 3.68e-05 (Fisher's exact test), Q value = 0.02

Table S25.  Gene #23: '12p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12P MUTATED 123 95 110
12P WILD-TYPE 49 80 111

Figure S25.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q' versus 'CN_CNMF'

P value = 2.84e-07 (Fisher's exact test), Q value = 0.00016

Table S26.  Gene #24: '12q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
12Q MUTATED 69 86 123
12Q WILD-TYPE 105 120 66

Figure S26.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #5: 'CN_CNMF'

'14q' versus 'CN_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.072

Table S27.  Gene #26: '14q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
14Q MUTATED 71 83 112
14Q WILD-TYPE 103 123 77

Figure S27.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'CN_CNMF'

'15q' versus 'MRNA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.19

Table S28.  Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
15Q MUTATED 141 103 63
15Q WILD-TYPE 74 113 63

Figure S28.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q' versus 'MRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.11

Table S29.  Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 210 219
15Q MUTATED 57 138 112
15Q WILD-TYPE 71 72 107

Figure S29.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 8.21e-11 (Fisher's exact test), Q value = 4.6e-08

Table S30.  Gene #27: '15q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
15Q MUTATED 77 96 142
15Q WILD-TYPE 97 110 47

Figure S30.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 4.43e-06 (Fisher's exact test), Q value = 0.0024

Table S31.  Gene #27: '15q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
15Q MUTATED 122 83 110
15Q WILD-TYPE 50 92 111

Figure S31.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q' versus 'CN_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.087

Table S32.  Gene #29: '16q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
16Q MUTATED 120 151 163
16Q WILD-TYPE 54 55 26

Figure S32.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #5: 'CN_CNMF'

'17q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000439 (Fisher's exact test), Q value = 0.23

Table S33.  Gene #31: '17q' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 195 157
17Q MUTATED 57 159 121
17Q WILD-TYPE 38 36 36

Figure S33.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'CN_CNMF'

P value = 9.98e-10 (Fisher's exact test), Q value = 5.5e-07

Table S34.  Gene #34: '19p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
19P MUTATED 90 108 150
19P WILD-TYPE 84 98 39

Figure S34.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #5: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 2.15e-05 (Fisher's exact test), Q value = 0.012

Table S35.  Gene #34: '19p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
19P MUTATED 128 89 130
19P WILD-TYPE 44 86 91

Figure S35.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q' versus 'CN_CNMF'

P value = 6.71e-08 (Fisher's exact test), Q value = 3.7e-05

Table S36.  Gene #35: '19q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
19Q MUTATED 93 98 141
19Q WILD-TYPE 81 108 48

Figure S36.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #5: 'CN_CNMF'

'20p' versus 'CN_CNMF'

P value = 7.04e-09 (Fisher's exact test), Q value = 3.9e-06

Table S37.  Gene #36: '20p' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
20P MUTATED 82 106 143
20P WILD-TYPE 92 100 46

Figure S37.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.00086

Table S38.  Gene #36: '20p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20P MUTATED 127 96 108
20P WILD-TYPE 45 79 113

Figure S38.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q' versus 'MRNA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S39.  Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
20Q MUTATED 152 112 80
20Q WILD-TYPE 63 104 46

Figure S39.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q' versus 'CN_CNMF'

P value = 3.71e-14 (Fisher's exact test), Q value = 2.1e-11

Table S40.  Gene #37: '20q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
20Q MUTATED 80 114 157
20Q WILD-TYPE 94 92 32

Figure S40.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #5: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.6e-09 (Fisher's exact test), Q value = 8.9e-07

Table S41.  Gene #37: '20q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20Q MUTATED 139 97 115
20Q WILD-TYPE 33 78 106

Figure S41.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q' versus 'CN_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.083

Table S42.  Gene #38: '21q' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
21Q MUTATED 79 101 124
21Q WILD-TYPE 95 105 65

Figure S42.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #5: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.078

Table S43.  Gene #38: '21q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
21Q MUTATED 114 79 110
21Q WILD-TYPE 58 96 111

Figure S43.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #6: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 569

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 14

  • Exclude genes that fewer than K tumors have alterations, 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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