Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1B27TR9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1B27TR9
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 79 arm-level events and 10 molecular subtypes across 56 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No arm-level cnvs related to molecular subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 24 (43%) 32 0.263
(0.818) 		0.598
(0.961) 		0.982
(1.00) 		0.799
(1.00) 		0.846
(1.00) 		0.903
(1.00) 		0.738
(0.998) 		0.367
(0.86) 		0.947
(1.00) 		0.67
(0.979)
1q gain 31 (55%) 25 0.941
(1.00) 		0.247
(0.81) 		0.872
(1.00) 		0.636
(0.97) 		0.563
(0.946) 		0.619
(0.97) 		0.737
(0.998) 		0.526
(0.93) 		0.764
(1.00) 		0.916
(1.00)
2p gain 23 (41%) 33 0.349
(0.86) 		0.106
(0.72) 		0.253
(0.81) 		0.0351
(0.697) 		0.0264
(0.688) 		0.0572
(0.707) 		0.304
(0.836) 		0.0722
(0.72) 		0.311
(0.836) 		0.134
(0.72)
2q gain 21 (38%) 35 0.361
(0.86) 		0.1
(0.72) 		0.211
(0.809) 		0.318
(0.844) 		0.00107
(0.45) 		0.112
(0.72) 		0.245
(0.81) 		0.0488
(0.707) 		0.364
(0.86) 		0.11
(0.72)
3p gain 10 (18%) 46 0.41
(0.864) 		0.79
(1.00) 		0.363
(0.86) 		0.297
(0.836) 		0.793
(1.00) 		0.248
(0.81) 		1
(1.00) 		0.467
(0.886) 		0.715
(0.997) 		0.408
(0.863)
3q gain 22 (39%) 34 0.101
(0.72) 		0.132
(0.72) 		0.382
(0.86) 		0.812
(1.00) 		0.456
(0.877) 		0.228
(0.81) 		0.22
(0.81) 		0.409
(0.863) 		0.813
(1.00) 		0.27
(0.825)
4p gain 10 (18%) 46 0.212
(0.809) 		0.596
(0.961) 		0.0133
(0.594) 		0.101
(0.72) 		0.637
(0.97) 		0.883
(1.00) 		0.407
(0.863) 		0.351
(0.86) 		1
(1.00) 		0.23
(0.81)
4q gain 3 (5%) 53 0.174
(0.786) 		0.392
(0.86) 		0.388
(0.86) 		0.793
(1.00) 		0.457
(0.877) 		0.568
(0.952) 		0.693
(0.991) 		0.699
(0.992)
5p gain 23 (41%) 33 0.479
(0.897) 		0.212
(0.809) 		0.0821
(0.72) 		0.199
(0.809) 		0.165
(0.786) 		0.243
(0.81) 		0.388
(0.86) 		0.0275
(0.688) 		0.583
(0.957) 		0.148
(0.744)
5q gain 8 (14%) 48 0.552
(0.944) 		0.511
(0.925) 		0.668
(0.978) 		0.208
(0.809) 		0.633
(0.97) 		0.248
(0.81) 		0.197
(0.809) 		0.152
(0.758) 		0.454
(0.877) 		0.193
(0.809)
6p gain 31 (55%) 25 0.231
(0.81) 		0.341
(0.86) 		0.497
(0.918) 		0.394
(0.86) 		0.933
(1.00) 		0.32
(0.844) 		0.581
(0.957) 		0.172
(0.786) 		0.523
(0.93) 		0.066
(0.707)
6q gain 27 (48%) 29 0.361
(0.86) 		0.24
(0.81) 		0.741
(0.998) 		0.623
(0.97) 		0.649
(0.97) 		0.166
(0.786) 		0.835
(1.00) 		0.189
(0.809) 		0.254
(0.81) 		0.137
(0.72)
7p gain 21 (38%) 35 0.779
(1.00) 		0.394
(0.86) 		0.561
(0.946) 		0.291
(0.836) 		0.223
(0.81) 		0.278
(0.836) 		0.383
(0.86) 		0.13
(0.72) 		0.342
(0.86) 		0.121
(0.72)
7q gain 18 (32%) 38 0.443
(0.877) 		0.806
(1.00) 		0.731
(0.998) 		0.607
(0.965) 		0.307
(0.836) 		0.66
(0.977) 		0.583
(0.957) 		0.111
(0.72) 		0.508
(0.925) 		0.0631
(0.707)
8p gain 18 (32%) 38 0.0882
(0.72) 		0.314
(0.838) 		0.0411
(0.698) 		0.173
(0.786) 		0.296
(0.836) 		0.774
(1.00) 		0.755
(1.00) 		0.385
(0.86) 		0.55
(0.944) 		0.23
(0.81)
8q gain 30 (54%) 26 0.062
(0.707) 		0.132
(0.72) 		0.38
(0.86) 		0.597
(0.961) 		0.0102
(0.573) 		0.508
(0.925) 		0.333
(0.859) 		0.325
(0.846) 		0.257
(0.81) 		0.122
(0.72)
9p gain 6 (11%) 50 1
(1.00) 		0.779
(1.00) 		0.506
(0.925) 		0.121
(0.72) 		0.935
(1.00) 		0.665
(0.977) 		0.867
(1.00) 		0.804
(1.00) 		0.784
(1.00) 		1
(1.00)
10p gain 20 (36%) 36 0.939
(1.00) 		0.58
(0.957) 		0.664
(0.977) 		0.544
(0.944) 		0.0262
(0.688) 		0.256
(0.81) 		0.626
(0.97) 		0.301
(0.836) 		0.319
(0.844) 		0.437
(0.877)
10q gain 17 (30%) 39 0.809
(1.00) 		0.885
(1.00) 		0.628
(0.97) 		0.462
(0.88) 		0.393
(0.86) 		0.0486
(0.707) 		0.221
(0.81) 		0.183
(0.804) 		0.19
(0.809) 		0.073
(0.72)
11p gain 5 (9%) 51 1
(1.00) 		0.758
(1.00) 		0.732
(0.998) 		0.925
(1.00) 		0.29
(0.836) 		0.854
(1.00) 		1
(1.00) 		0.119
(0.72) 		0.382
(0.86) 		0.0922
(0.72)
11q gain 7 (12%) 49 0.272
(0.826) 		0.95
(1.00) 		0.193
(0.809) 		0.717
(0.997) 		0.16
(0.786) 		0.38
(0.86) 		0.447
(0.877) 		0.0356
(0.697) 		0.679
(0.985) 		0.0304
(0.697)
12p gain 22 (39%) 34 0.395
(0.86) 		0.019
(0.645) 		0.382
(0.86) 		0.593
(0.961) 		0.183
(0.804) 		0.0428
(0.704) 		0.883
(1.00) 		0.977
(1.00) 		0.813
(1.00) 		0.627
(0.97)
12q gain 11 (20%) 45 0.439
(0.877) 		0.536
(0.935) 		0.966
(1.00) 		0.855
(1.00) 		0.627
(0.97) 		0.523
(0.93) 		0.687
(0.988) 		0.297
(0.836) 		0.642
(0.97) 		0.27
(0.825)
13q gain 15 (27%) 41 1
(1.00) 		0.306
(0.836) 		0.0947
(0.72) 		0.545
(0.944) 		0.037
(0.697) 		0.0245
(0.688) 		0.0348
(0.697) 		0.0461
(0.707) 		0.0591
(0.707) 		0.141
(0.72)
14q gain 7 (12%) 49 0.45
(0.877) 		0.106
(0.72) 		0.437
(0.877) 		0.0499
(0.707) 		0.209
(0.809) 		0.259
(0.811) 		0.257
(0.81) 		0.735
(0.998) 		0.118
(0.72) 		0.473
(0.889)
15q gain 4 (7%) 52 0.347
(0.86) 		0.352
(0.86) 		0.229
(0.81) 		0.581
(0.957) 		0.403
(0.863) 		0.329
(0.856) 		0.0537
(0.707) 		0.346
(0.86) 		0.574
(0.957) 		0.356
(0.86)
16p gain 10 (18%) 46 0.00682
(0.45) 		0.701
(0.993) 		0.534
(0.935) 		0.828
(1.00) 		0.217
(0.81) 		0.279
(0.836) 		0.739
(0.998) 		0.483
(0.9) 		0.591
(0.961) 		0.406
(0.863)
16q gain 6 (11%) 50 0.0555
(0.707) 		0.483
(0.9) 		0.919
(1.00) 		0.926
(1.00) 		0.513
(0.926) 		0.969
(1.00) 		1
(1.00) 		0.925
(1.00) 		1
(1.00) 		0.867
(1.00)
17p gain 9 (16%) 47 0.651
(0.97) 		0.63
(0.97) 		0.886
(1.00) 		0.826
(1.00) 		0.646
(0.97) 		0.562
(0.946) 		0.301
(0.836) 		0.0615
(0.707) 		0.763
(1.00) 		0.172
(0.786)
17q gain 18 (32%) 38 0.767
(1.00) 		0.743
(0.998) 		0.724
(0.998) 		0.804
(1.00) 		0.648
(0.97) 		0.511
(0.925) 		0.666
(0.977) 		0.307
(0.836) 		0.711
(0.997) 		0.429
(0.877)
18p gain 18 (32%) 38 0.819
(1.00) 		0.347
(0.86) 		0.685
(0.988) 		0.786
(1.00) 		0.0568
(0.707) 		0.343
(0.86) 		0.119
(0.72) 		0.2
(0.809) 		0.405
(0.863) 		0.433
(0.877)
18q gain 13 (23%) 43 0.729
(0.998) 		0.945
(1.00) 		0.683
(0.988) 		0.601
(0.961) 		0.181
(0.804) 		0.291
(0.836) 		0.236
(0.81) 		0.173
(0.786) 		0.251
(0.81) 		0.285
(0.836)
19p gain 24 (43%) 32 0.107
(0.72) 		0.522
(0.93) 		0.486
(0.903) 		0.78
(1.00) 		0.118
(0.72) 		0.185
(0.804) 		0.115
(0.72) 		0.0391
(0.698) 		0.22
(0.81) 		0.139
(0.72)
19q gain 29 (52%) 27 0.121
(0.72) 		0.689
(0.988) 		0.658
(0.977) 		0.873
(1.00) 		0.81
(1.00) 		0.435
(0.877) 		0.834
(1.00) 		0.773
(1.00) 		0.716
(0.997) 		0.978
(1.00)
20p gain 36 (64%) 20 0.46
(0.878) 		0.734
(0.998) 		0.0661
(0.707) 		0.471
(0.889) 		0.779
(1.00) 		0.727
(0.998) 		0.554
(0.944) 		0.35
(0.86) 		0.186
(0.804) 		0.21
(0.809)
20q gain 43 (77%) 13 0.168
(0.786) 		0.742
(0.998) 		0.207
(0.809) 		0.713
(0.997) 		0.829
(1.00) 		0.95
(1.00) 		0.44
(0.877) 		0.24
(0.81) 		0.214
(0.809) 		0.391
(0.86)
21q gain 18 (32%) 38 0.015
(0.594) 		0.113
(0.72) 		0.214
(0.809) 		0.788
(1.00) 		0.923
(1.00) 		0.891
(1.00) 		0.353
(0.86) 		0.571
(0.953) 		1
(1.00) 		0.947
(1.00)
22q gain 8 (14%) 48 0.49
(0.908) 		0.915
(1.00) 		0.528
(0.931) 		0.305
(0.836) 		0.77
(1.00) 		0.927
(1.00) 		0.892
(1.00) 		0.943
(1.00) 		0.949
(1.00) 		1
(1.00)
xp gain 18 (32%) 38 0.667
(0.977) 		0.0383
(0.698) 		0.602
(0.961) 		0.341
(0.86) 		0.0644
(0.707) 		0.456
(0.877) 		1
(1.00) 		0.56
(0.946) 		0.271
(0.825) 		0.434
(0.877)
xq gain 15 (27%) 41 0.863
(1.00) 		0.417
(0.872) 		0.887
(1.00) 		0.246
(0.81) 		0.525
(0.93) 		0.542
(0.943) 		0.173
(0.786) 		0.292
(0.836) 		0.0861
(0.72) 		0.203
(0.809)
1p loss 10 (18%) 46 0.408
(0.863) 		0.791
(1.00) 		0.945
(1.00) 		0.456
(0.877) 		0.84
(1.00) 		0.101
(0.72) 		0.0366
(0.697) 		0.0139
(0.594) 		0.517
(0.93) 		0.0146
(0.594)
1q loss 10 (18%) 46 0.242
(0.81) 		0.704
(0.995) 		0.649
(0.97) 		0.197
(0.809) 		0.699
(0.992) 		0.0983
(0.72) 		0.137
(0.72) 		0.0703
(0.72) 		0.415
(0.872) 		0.0894
(0.72)
3p loss 22 (39%) 34 0.449
(0.877) 		0.452
(0.877) 		0.438
(0.877) 		0.583
(0.957) 		0.0196
(0.645) 		0.167
(0.786) 		0.729
(0.998) 		0.953
(1.00) 		0.678
(0.985) 		0.663
(0.977)
3q loss 15 (27%) 41 0.204
(0.809) 		0.347
(0.86) 		0.509
(0.925) 		0.862
(1.00) 		0.0655
(0.707) 		0.407
(0.863) 		0.168
(0.786) 		0.911
(1.00) 		0.974
(1.00) 		0.97
(1.00)
4p loss 30 (54%) 26 0.129
(0.72) 		0.00917
(0.557) 		0.00427
(0.45) 		0.0751
(0.72) 		0.518
(0.93) 		0.442
(0.877) 		0.422
(0.873) 		0.634
(0.97) 		0.099
(0.72) 		0.46
(0.878)
4q loss 34 (61%) 22 0.205
(0.809) 		0.00383
(0.45) 		0.12
(0.72) 		0.2
(0.809) 		0.0248
(0.688) 		0.057
(0.707) 		0.00361
(0.45) 		0.208
(0.809) 		0.00506
(0.45) 		0.0774
(0.72)
5p loss 9 (16%) 47 1
(1.00) 		0.253
(0.81) 		0.0348
(0.697) 		0.0623
(0.707) 		0.796
(1.00) 		0.133
(0.72) 		1
(1.00) 		0.298
(0.836) 		1
(1.00) 		0.419
(0.872)
5q loss 18 (32%) 38 0.765
(1.00) 		0.114
(0.72) 		0.794
(1.00) 		0.0791
(0.72) 		0.355
(0.86) 		0.234
(0.81) 		1
(1.00) 		0.948
(1.00) 		0.549
(0.944) 		0.948
(1.00)
6p loss 5 (9%) 51 0.225
(0.81) 		0.918
(1.00) 		0.137
(0.72) 		0.752
(1.00) 		0.801
(1.00) 		0.957
(1.00) 		1
(1.00) 		0.912
(1.00) 		0.923
(1.00) 		1
(1.00)
6q loss 7 (12%) 49 0.0821
(0.72) 		1
(1.00) 		0.226
(0.81) 		0.13
(0.72) 		0.449
(0.877) 		0.921
(1.00) 		1
(1.00) 		0.936
(1.00) 		0.626
(0.97) 		0.934
(1.00)
7p loss 13 (23%) 43 0.512
(0.925) 		0.708
(0.997) 		0.266
(0.823) 		0.289
(0.836) 		0.678
(0.985) 		0.498
(0.918) 		0.85
(1.00) 		0.455
(0.877) 		0.476
(0.893) 		0.598
(0.961)
7q loss 12 (21%) 44 0.134
(0.72) 		0.97
(1.00) 		0.586
(0.957) 		0.618
(0.97) 		0.969
(1.00) 		0.944
(1.00) 		0.65
(0.97) 		0.308
(0.836) 		0.463
(0.88) 		0.554
(0.944)
8p loss 24 (43%) 32 0.0415
(0.698) 		0.948
(1.00) 		0.42
(0.872) 		0.138
(0.72) 		0.915
(1.00) 		0.619
(0.97) 		1
(1.00) 		0.367
(0.86) 		0.947
(1.00) 		0.348
(0.86)
8q loss 9 (16%) 47 0.371
(0.86) 		0.674
(0.983) 		0.812
(1.00) 		0.688
(0.988) 		0.0399
(0.698) 		0.712
(0.997) 		0.897
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.666
(0.977)
9p loss 35 (62%) 21 0.112
(0.72) 		0.27
(0.825) 		0.00683
(0.45) 		0.00217
(0.45) 		0.644
(0.97) 		0.213
(0.809) 		0.587
(0.957) 		0.382
(0.86) 		0.319
(0.844) 		0.0919
(0.72)
9q loss 40 (71%) 16 0.0662
(0.707) 		0.309
(0.836) 		0.0801
(0.72) 		0.0658
(0.707) 		0.874
(1.00) 		0.0588
(0.707) 		0.688
(0.988) 		0.223
(0.81) 		0.73
(0.998) 		0.252
(0.81)
10p loss 24 (43%) 32 0.619
(0.97) 		0.0366
(0.697) 		0.717
(0.997) 		0.806
(1.00) 		0.0178
(0.645) 		0.224
(0.81) 		1
(1.00) 		1
(1.00) 		0.886
(1.00) 		0.976
(1.00)
10q loss 20 (36%) 36 0.937
(1.00) 		0.447
(0.877) 		0.428
(0.877) 		0.783
(1.00) 		0.386
(0.86) 		0.257
(0.81) 		0.63
(0.97) 		0.588
(0.957) 		0.354
(0.86) 		0.824
(1.00)
11p loss 28 (50%) 28 0.786
(1.00) 		0.0253
(0.688) 		0.605
(0.964) 		0.89
(1.00) 		0.733
(0.998) 		0.312
(0.836) 		0.334
(0.859) 		0.391
(0.86) 		0.323
(0.845) 		0.231
(0.81)
11q loss 26 (46%) 30 0.137
(0.72) 		0.436
(0.877) 		0.115
(0.72) 		0.91
(1.00) 		0.845
(1.00) 		0.535
(0.935) 		0.377
(0.86) 		0.526
(0.93) 		0.249
(0.81) 		0.137
(0.72)
12p loss 13 (23%) 43 0.375
(0.86) 		0.648
(0.97) 		0.284
(0.836) 		0.743
(0.998) 		0.721
(0.998) 		0.734
(0.998) 		0.783
(1.00) 		0.578
(0.957) 		0.775
(1.00) 		0.217
(0.81)
12q loss 14 (25%) 42 0.307
(0.836) 		0.973
(1.00) 		0.419
(0.872) 		0.125
(0.72) 		0.883
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.395
(0.86) 		0.602
(0.961)
13q loss 26 (46%) 30 0.52
(0.93) 		0.0702
(0.72) 		0.304
(0.836) 		0.149
(0.744) 		0.0979
(0.72) 		0.0278
(0.688) 		0.4
(0.863) 		0.118
(0.72) 		0.13
(0.72) 		0.199
(0.809)
14q loss 27 (48%) 29 0.942
(1.00) 		0.174
(0.786) 		0.866
(1.00) 		0.117
(0.72) 		0.107
(0.72) 		0.124
(0.72) 		0.382
(0.86) 		0.898
(1.00) 		0.285
(0.836) 		0.938
(1.00)
15q loss 33 (59%) 23 0.0111
(0.584) 		0.347
(0.86) 		0.903
(1.00) 		0.126
(0.72) 		1
(1.00) 		0.98
(1.00) 		1
(1.00) 		0.953
(1.00) 		0.878
(1.00) 		0.91
(1.00)
16p loss 32 (57%) 24 0.421
(0.873) 		0.823
(1.00) 		0.404
(0.863) 		0.086
(0.72) 		0.322
(0.845) 		0.0989
(0.72) 		0.37
(0.86) 		0.915
(1.00) 		0.869
(1.00) 		0.896
(1.00)
16q loss 37 (66%) 19 0.369
(0.86) 		0.373
(0.86) 		0.25
(0.81) 		0.129
(0.72) 		0.645
(0.97) 		0.0903
(0.72) 		0.141
(0.72) 		0.922
(1.00) 		0.882
(1.00) 		0.859
(1.00)
17p loss 34 (61%) 22 0.445
(0.877) 		0.345
(0.86) 		0.0196
(0.645) 		0.274
(0.829) 		0.927
(1.00) 		0.759
(1.00) 		0.939
(1.00) 		0.891
(1.00) 		0.444
(0.877) 		0.889
(1.00)
17q loss 17 (30%) 39 0.659
(0.977) 		0.553
(0.944) 		0.132
(0.72) 		0.628
(0.97) 		0.695
(0.991) 		0.385
(0.86) 		0.26
(0.811) 		0.212
(0.809) 		0.738
(0.998) 		0.276
(0.834)
18p loss 18 (32%) 38 0.473
(0.889) 		0.252
(0.81) 		0.559
(0.946) 		0.291
(0.836) 		0.0469
(0.707) 		0.09
(0.72) 		0.0321
(0.697) 		0.0789
(0.72) 		0.0816
(0.72) 		0.0464
(0.707)
18q loss 20 (36%) 36 0.147
(0.743) 		0.597
(0.961) 		0.298
(0.836) 		0.297
(0.836) 		0.246
(0.81) 		0.12
(0.72) 		0.00142
(0.45) 		0.00553
(0.45) 		0.0654
(0.707) 		0.00255
(0.45)
19p loss 15 (27%) 41 0.55
(0.944) 		0.141
(0.72) 		0.158
(0.779) 		0.38
(0.86) 		0.0127
(0.594) 		0.0613
(0.707) 		0.166
(0.786) 		0.254
(0.81) 		0.0906
(0.72) 		0.186
(0.804)
19q loss 12 (21%) 44 0.65
(0.97) 		0.629
(0.97) 		0.105
(0.72) 		0.816
(1.00) 		0.842
(1.00) 		0.508
(0.925) 		0.408
(0.863) 		0.961
(1.00) 		0.57
(0.953) 		1
(1.00)
20p loss 8 (14%) 48 0.889
(1.00) 		0.587
(0.957) 		0.532
(0.935) 		0.00627
(0.45) 		0.18
(0.802) 		0.285
(0.836) 		0.557
(0.946) 		0.335
(0.859) 		0.838
(1.00) 		0.395
(0.86)
20q loss 5 (9%) 51 0.434
(0.877) 		0.806
(1.00) 		0.786
(1.00) 		0.241
(0.81) 		0.536
(0.935) 		0.911
(1.00) 		0.71
(0.997) 		0.694
(0.991) 		1
(1.00) 		0.627
(0.97)
21q loss 17 (30%) 39 0.431
(0.877) 		0.0776
(0.72) 		0.0567
(0.707) 		0.33
(0.856) 		0.491
(0.909) 		0.747
(1.00) 		0.807
(1.00) 		0.973
(1.00) 		1
(1.00) 		0.942
(1.00)
22q loss 33 (59%) 23 0.942
(1.00) 		0.899
(1.00) 		0.394
(0.86) 		0.0217
(0.686) 		0.779
(1.00) 		0.901
(1.00) 		0.179
(0.802) 		0.29
(0.836) 		0.945
(1.00) 		0.759
(1.00)
xp loss 15 (27%) 41 0.191
(0.809) 		0.698
(0.992) 		0.924
(1.00) 		0.17
(0.786) 		0.952
(1.00) 		0.859
(1.00) 		0.547
(0.944) 		0.647
(0.97) 		0.829
(1.00) 		0.761
(1.00)
xq loss 18 (32%) 38 0.766
(1.00) 		0.854
(1.00) 		0.868
(1.00) 		0.0341
(0.697) 		0.428
(0.877) 		0.624
(0.97) 		0.311
(0.836) 		0.647
(0.97) 		0.137
(0.72) 		0.752
(1.00)
Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/22533738/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/22541488/UCS-TP.transferedmergedcluster.txt

  • Number of patients = 56

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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