Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1C53JKK
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/C1C53JKK
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 77 arm-level events and 8 molecular subtypes across 56 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.

  • 4q loss cnv correlated to 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 77 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, one significant finding detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type 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
4q loss 33 (59%) 23 0.0654
(1.00) 		0.0196
(1.00) 		0.00525
(1.00) 		0.0104
(1.00) 		0.000195
(0.12) 		0.218
(1.00) 		0.0184
(1.00) 		0.101
(1.00)
1p gain 24 (43%) 32 0.0443
(1.00) 		0.738
(1.00) 		0.795
(1.00) 		0.801
(1.00) 		0.518
(1.00) 		0.0796
(1.00) 		0.611
(1.00) 		0.366
(1.00)
1q gain 31 (55%) 25 0.305
(1.00) 		0.739
(1.00) 		0.747
(1.00) 		0.414
(1.00) 		0.663
(1.00) 		0.552
(1.00) 		0.952
(1.00) 		1
(1.00)
2p gain 23 (41%) 33 0.758
(1.00) 		0.00996
(1.00) 		0.02
(1.00) 		0.0503
(1.00) 		0.477
(1.00) 		0.0395
(1.00) 		0.281
(1.00) 		0.0293
(1.00)
2q gain 21 (38%) 35 0.612
(1.00) 		0.0171
(1.00) 		0.0125
(1.00) 		0.0255
(1.00) 		0.579
(1.00) 		0.0314
(1.00) 		0.378
(1.00) 		0.0269
(1.00)
3p gain 12 (21%) 44 0.369
(1.00) 		0.25
(1.00) 		0.435
(1.00) 		0.382
(1.00) 		0.861
(1.00) 		0.415
(1.00) 		0.959
(1.00) 		0.485
(1.00)
3q gain 23 (41%) 33 0.209
(1.00) 		0.0444
(1.00) 		0.197
(1.00) 		0.169
(1.00) 		0.477
(1.00) 		0.326
(1.00) 		0.492
(1.00) 		0.246
(1.00)
4p gain 9 (16%) 47 1
(1.00) 		0.571
(1.00) 		0.823
(1.00) 		0.814
(1.00) 		0.776
(1.00) 		0.557
(1.00) 		0.825
(1.00) 		0.764
(1.00)
4q gain 3 (5%) 53 0.581
(1.00) 		0.278
(1.00) 		0.513
(1.00) 		0.491
(1.00) 		0.673
(1.00) 		1
(1.00) 		0.687
(1.00) 		1
(1.00)
5p gain 23 (41%) 33 0.376
(1.00) 		0.366
(1.00) 		0.431
(1.00) 		0.377
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.894
(1.00) 		0.704
(1.00)
5q gain 8 (14%) 48 0.781
(1.00) 		0.557
(1.00) 		0.309
(1.00) 		0.297
(1.00) 		0.0803
(1.00) 		0.0934
(1.00) 		0.24
(1.00) 		0.221
(1.00)
6p gain 30 (54%) 26 0.312
(1.00) 		0.504
(1.00) 		0.601
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.892
(1.00) 		0.64
(1.00)
6q gain 27 (48%) 29 0.351
(1.00) 		0.199
(1.00) 		0.219
(1.00) 		0.0382
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.809
(1.00) 		1
(1.00)
7p gain 21 (38%) 35 0.519
(1.00) 		0.539
(1.00) 		0.143
(1.00) 		0.133
(1.00) 		0.565
(1.00) 		0.449
(1.00) 		0.373
(1.00) 		0.227
(1.00)
7q gain 17 (30%) 39 0.424
(1.00) 		0.833
(1.00) 		0.335
(1.00) 		0.745
(1.00) 		0.685
(1.00) 		0.509
(1.00) 		0.57
(1.00) 		0.723
(1.00)
8p gain 19 (34%) 37 0.0125
(1.00) 		0.718
(1.00) 		0.438
(1.00) 		0.659
(1.00) 		0.952
(1.00) 		0.299
(1.00) 		0.804
(1.00) 		0.624
(1.00)
8q gain 30 (54%) 26 0.00509
(1.00) 		0.184
(1.00) 		0.0477
(1.00) 		0.309
(1.00) 		0.224
(1.00) 		0.446
(1.00) 		0.218
(1.00) 		0.116
(1.00)
9p gain 6 (11%) 50 0.465
(1.00) 		0.619
(1.00) 		0.936
(1.00) 		0.358
(1.00) 		0.832
(1.00) 		0.477
(1.00) 		0.798
(1.00) 		0.71
(1.00)
10p gain 21 (38%) 35 0.891
(1.00) 		0.0284
(1.00) 		0.0413
(1.00) 		0.254
(1.00) 		0.317
(1.00) 		0.808
(1.00) 		0.519
(1.00) 		0.57
(1.00)
10q gain 17 (30%) 39 1
(1.00) 		0.293
(1.00) 		0.552
(1.00) 		0.311
(1.00) 		0.205
(1.00) 		0.513
(1.00) 		0.412
(1.00) 		0.216
(1.00)
11p gain 5 (9%) 51 0.483
(1.00) 		0.407
(1.00) 		0.265
(1.00) 		0.515
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.352
(1.00) 		1
(1.00)
11q gain 7 (12%) 49 0.17
(1.00) 		0.337
(1.00) 		0.226
(1.00) 		0.605
(1.00) 		0.755
(1.00) 		0.738
(1.00) 		0.726
(1.00) 		1
(1.00)
12p gain 22 (39%) 34 0.44
(1.00) 		0.00524
(1.00) 		0.376
(1.00) 		0.132
(1.00) 		0.783
(1.00) 		0.83
(1.00) 		0.762
(1.00) 		0.779
(1.00)
12q gain 11 (20%) 45 0.555
(1.00) 		0.503
(1.00) 		0.805
(1.00) 		0.708
(1.00) 		1
(1.00) 		0.403
(1.00) 		0.529
(1.00) 		0.57
(1.00)
13q gain 15 (27%) 41 0.663
(1.00) 		0.061
(1.00) 		0.0222
(1.00) 		0.0645
(1.00) 		0.228
(1.00) 		0.0108
(1.00) 		0.0655
(1.00) 		0.0157
(1.00)
14q gain 7 (12%) 49 0.365
(1.00) 		0.475
(1.00) 		0.258
(1.00) 		0.444
(1.00) 		0.206
(1.00) 		0.0616
(1.00) 		0.213
(1.00) 		0.0355
(1.00)
15q gain 4 (7%) 52 0.389
(1.00) 		0.36
(1.00) 		0.577
(1.00) 		0.503
(1.00) 		0.755
(1.00) 		0.39
(1.00) 		0.53
(1.00) 		0.643
(1.00)
16p gain 10 (18%) 46 0.0396
(1.00) 		0.256
(1.00) 		0.195
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.115
(1.00) 		0.716
(1.00) 		0.157
(1.00)
16q gain 6 (11%) 50 0.269
(1.00) 		0.768
(1.00) 		0.547
(1.00) 		0.87
(1.00) 		0.771
(1.00) 		0.706
(1.00) 		0.917
(1.00) 		1
(1.00)
17p gain 9 (16%) 47 0.215
(1.00) 		0.832
(1.00) 		0.568
(1.00) 		0.653
(1.00) 		0.285
(1.00) 		0.557
(1.00) 		0.271
(1.00) 		0.393
(1.00)
17q gain 18 (32%) 38 0.88
(1.00) 		0.246
(1.00) 		0.7
(1.00) 		0.716
(1.00) 		0.394
(1.00) 		0.48
(1.00) 		0.704
(1.00) 		0.277
(1.00)
18p gain 18 (32%) 38 1
(1.00) 		0.0416
(1.00) 		0.0952
(1.00) 		0.0322
(1.00) 		0.152
(1.00) 		0.621
(1.00) 		0.411
(1.00) 		0.3
(1.00)
18q gain 14 (25%) 42 0.635
(1.00) 		0.111
(1.00) 		0.153
(1.00) 		0.0652
(1.00) 		0.199
(1.00) 		0.378
(1.00) 		0.21
(1.00) 		0.0518
(1.00)
19p gain 24 (43%) 32 0.501
(1.00) 		0.18
(1.00) 		0.254
(1.00) 		0.826
(1.00) 		0.524
(1.00) 		0.472
(1.00) 		0.389
(1.00) 		0.3
(1.00)
19q gain 28 (50%) 28 0.32
(1.00) 		0.0705
(1.00) 		0.357
(1.00) 		0.575
(1.00) 		0.891
(1.00) 		1
(1.00) 		0.535
(1.00) 		1
(1.00)
20p gain 37 (66%) 19 0.906
(1.00) 		0.486
(1.00) 		0.923
(1.00) 		0.345
(1.00) 		0.852
(1.00) 		0.537
(1.00) 		0.843
(1.00) 		0.548
(1.00)
20q gain 44 (79%) 12 0.493
(1.00) 		0.892
(1.00) 		0.969
(1.00) 		0.861
(1.00) 		0.582
(1.00) 		0.336
(1.00) 		0.432
(1.00) 		0.465
(1.00)
21q gain 18 (32%) 38 0.207
(1.00) 		0.375
(1.00) 		0.901
(1.00) 		0.767
(1.00) 		0.882
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.624
(1.00)
22q gain 8 (14%) 48 0.535
(1.00) 		0.927
(1.00) 		0.804
(1.00) 		0.791
(1.00) 		0.887
(1.00) 		0.539
(1.00) 		0.852
(1.00) 		0.753
(1.00)
xq gain 14 (25%) 42 0.896
(1.00) 		0.453
(1.00) 		0.88
(1.00) 		0.574
(1.00) 		0.962
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.63
(1.00)
1p loss 9 (16%) 47 0.0519
(1.00) 		0.613
(1.00) 		0.921
(1.00) 		0.957
(1.00) 		0.111
(1.00) 		0.0169
(1.00) 		0.125
(1.00) 		0.0442
(1.00)
1q loss 9 (16%) 47 0.0238
(1.00) 		0.525
(1.00) 		0.515
(1.00) 		0.49
(1.00) 		0.421
(1.00) 		0.136
(1.00) 		0.386
(1.00) 		0.292
(1.00)
3p loss 20 (36%) 36 0.0711
(1.00) 		0.376
(1.00) 		0.0499
(1.00) 		0.0581
(1.00) 		0.352
(1.00) 		0.377
(1.00) 		0.603
(1.00) 		0.39
(1.00)
3q loss 14 (25%) 42 0.514
(1.00) 		0.467
(1.00) 		0.137
(1.00) 		0.246
(1.00) 		0.498
(1.00) 		0.181
(1.00) 		0.653
(1.00) 		0.215
(1.00)
4p loss 31 (55%) 25 0.0591
(1.00) 		0.0596
(1.00) 		0.255
(1.00) 		0.131
(1.00) 		0.042
(1.00) 		0.699
(1.00) 		0.28
(1.00) 		0.541
(1.00)
5p loss 9 (16%) 47 0.712
(1.00) 		0.476
(1.00) 		0.885
(1.00) 		0.557
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
5q loss 18 (32%) 38 0.88
(1.00) 		0.308
(1.00) 		0.264
(1.00) 		0.187
(1.00) 		0.36
(1.00) 		0.784
(1.00) 		0.152
(1.00) 		1
(1.00)
6p loss 5 (9%) 51 0.315
(1.00) 		0.811
(1.00) 		0.755
(1.00) 		0.916
(1.00) 		0.544
(1.00) 		0.694
(1.00) 		0.745
(1.00) 		1
(1.00)
6q loss 7 (12%) 49 0.0186
(1.00) 		0.577
(1.00) 		0.64
(1.00) 		0.552
(1.00) 		0.705
(1.00) 		0.0616
(1.00) 		0.726
(1.00) 		0.121
(1.00)
7p loss 13 (23%) 43 0.416
(1.00) 		0.617
(1.00) 		0.736
(1.00) 		0.696
(1.00) 		0.309
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.629
(1.00)
7q loss 13 (23%) 43 0.0864
(1.00) 		0.826
(1.00) 		0.92
(1.00) 		0.664
(1.00) 		0.688
(1.00) 		0.56
(1.00) 		0.639
(1.00) 		1
(1.00)
8p loss 23 (41%) 33 0.0273
(1.00) 		0.974
(1.00) 		0.804
(1.00) 		0.958
(1.00) 		0.666
(1.00) 		0.293
(1.00) 		0.819
(1.00) 		0.655
(1.00)
8q loss 9 (16%) 47 0.187
(1.00) 		0.752
(1.00) 		0.296
(1.00) 		0.753
(1.00) 		0.95
(1.00) 		1
(1.00) 		1
(1.00) 		0.764
(1.00)
9p loss 34 (61%) 22 0.0377
(1.00) 		0.0146
(1.00) 		0.66
(1.00) 		0.624
(1.00) 		0.829
(1.00) 		0.755
(1.00) 		0.826
(1.00) 		1
(1.00)
9q loss 39 (70%) 17 0.0621
(1.00) 		0.00331
(1.00) 		0.493
(1.00) 		0.674
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.779
(1.00)
10p loss 23 (41%) 33 0.859
(1.00) 		0.0126
(1.00) 		0.0304
(1.00) 		0.0575
(1.00) 		0.239
(1.00) 		0.736
(1.00) 		0.421
(1.00) 		0.825
(1.00)
10q loss 21 (38%) 35 1
(1.00) 		0.296
(1.00) 		0.176
(1.00) 		0.251
(1.00) 		0.128
(1.00) 		0.755
(1.00) 		0.188
(1.00) 		0.176
(1.00)
11p loss 26 (46%) 30 0.833
(1.00) 		0.00422
(1.00) 		0.377
(1.00) 		0.516
(1.00) 		0.259
(1.00) 		0.446
(1.00) 		0.241
(1.00) 		0.309
(1.00)
11q loss 24 (43%) 32 0.724
(1.00) 		0.00885
(1.00) 		0.79
(1.00) 		0.86
(1.00) 		0.286
(1.00) 		0.194
(1.00) 		0.386
(1.00) 		0.366
(1.00)
12p loss 13 (23%) 43 0.195
(1.00) 		0.297
(1.00) 		0.579
(1.00) 		0.804
(1.00) 		0.546
(1.00) 		0.103
(1.00) 		0.274
(1.00) 		0.328
(1.00)
12q loss 14 (25%) 42 0.5
(1.00) 		0.854
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.958
(1.00) 		0.181
(1.00) 		0.456
(1.00) 		0.361
(1.00)
13q loss 26 (46%) 30 0.775
(1.00) 		0.00156
(0.957) 		0.0567
(1.00) 		0.104
(1.00) 		0.356
(1.00) 		0.193
(1.00) 		0.251
(1.00) 		0.107
(1.00)
14q loss 27 (48%) 29 1
(1.00) 		0.0995
(1.00) 		0.114
(1.00) 		0.217
(1.00) 		0.569
(1.00) 		0.598
(1.00) 		0.575
(1.00) 		1
(1.00)
15q loss 32 (57%) 24 0.00613
(1.00) 		0.693
(1.00) 		0.893
(1.00) 		0.757
(1.00) 		0.871
(1.00) 		0.765
(1.00) 		0.881
(1.00) 		0.825
(1.00)
16p loss 32 (57%) 24 0.35
(1.00) 		0.465
(1.00) 		0.324
(1.00) 		0.189
(1.00) 		0.789
(1.00) 		0.519
(1.00) 		0.881
(1.00) 		0.467
(1.00)
16q loss 37 (66%) 19 0.318
(1.00) 		0.768
(1.00) 		0.449
(1.00) 		0.392
(1.00) 		0.692
(1.00) 		0.784
(1.00) 		0.359
(1.00) 		0.779
(1.00)
17p loss 34 (61%) 22 0.397
(1.00) 		0.278
(1.00) 		0.958
(1.00) 		0.884
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.671
(1.00)
17q loss 17 (30%) 39 0.893
(1.00) 		0.331
(1.00) 		0.715
(1.00) 		0.257
(1.00) 		0.903
(1.00) 		0.451
(1.00) 		0.766
(1.00) 		1
(1.00)
18p loss 18 (32%) 38 0.556
(1.00) 		0.0127
(1.00) 		0.0535
(1.00) 		0.0356
(1.00) 		0.0634
(1.00) 		0.197
(1.00) 		0.313
(1.00) 		0.0514
(1.00)
18q loss 20 (36%) 36 0.212
(1.00) 		0.054
(1.00) 		0.181
(1.00) 		0.0272
(1.00) 		0.013
(1.00) 		0.0122
(1.00) 		0.0634
(1.00) 		0.00158
(0.972)
19p loss 15 (27%) 41 0.914
(1.00) 		0.427
(1.00) 		0.203
(1.00) 		0.103
(1.00) 		0.313
(1.00) 		1
(1.00) 		0.713
(1.00) 		1
(1.00)
19q loss 13 (23%) 43 1
(1.00) 		0.112
(1.00) 		0.945
(1.00) 		0.784
(1.00) 		0.232
(1.00) 		0.704
(1.00) 		0.693
(1.00) 		0.629
(1.00)
20p loss 7 (12%) 49 0.429
(1.00) 		0.257
(1.00) 		0.0816
(1.00) 		0.0871
(1.00) 		0.617
(1.00) 		0.738
(1.00) 		0.726
(1.00) 		0.503
(1.00)
20q loss 4 (7%) 52 1
(1.00) 		0.523
(1.00) 		0.117
(1.00) 		0.454
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 17 (30%) 39 0.843
(1.00) 		0.187
(1.00) 		0.632
(1.00) 		0.873
(1.00) 		0.637
(1.00) 		0.733
(1.00) 		1
(1.00) 		1
(1.00)
22q loss 33 (59%) 23 0.859
(1.00) 		0.969
(1.00) 		0.94
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.242
(1.00) 		0.607
(1.00) 		0.305
(1.00)
xq loss 19 (34%) 37 0.44
(1.00) 		0.299
(1.00) 		0.326
(1.00) 		0.541
(1.00) 		0.53
(1.00) 		1
(1.00) 		0.543
(1.00) 		1
(1.00)
'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #45: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 22 4 19
4Q LOSS MUTATED 10 16 0 7
4Q LOSS WILD-TYPE 0 6 4 12

Figure S1.  Get High-res Image Gene #45: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 56

  • Number of significantly arm-level cnvs = 77

  • Number of molecular subtypes = 8

  • 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

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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