Head and Neck Squamous Cell Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 79 arm-level results and 11 clinical features across 305 patients, one significant finding detected with Q value < 0.25.

  • 18p gain cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE GENDER PATHOLOGY
T 		PATHOLOGY
N 		TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED STOPPEDSMOKINGYEAR TOBACCOSMOKINGHISTORYINDICATOR YEAROFTOBACCOSMOKINGONSET
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test t-test
18p gain 51 (17%) 254 0.219
(1.00) 		0.431
(1.00) 		0.000263
(0.228) 		0.00644
(1.00) 		0.531
(1.00) 		0.0349
(1.00) 		0.38
(1.00) 		0.195
(1.00) 		0.272
(1.00) 		0.363
(1.00) 		0.775
(1.00)
1p gain 11 (4%) 294 0.782
(1.00) 		0.546
(1.00) 		0.0772
(1.00) 		0.349
(1.00) 		0.747
(1.00) 		0.888
(1.00) 		0.737
(1.00) 		0.426
(1.00) 		0.11
(1.00) 		0.0183
(1.00) 		0.885
(1.00)
1q gain 38 (12%) 267 0.843
(1.00) 		0.691
(1.00) 		0.563
(1.00) 		0.134
(1.00) 		0.0154
(1.00) 		0.0929
(1.00) 		0.164
(1.00) 		0.96
(1.00) 		0.225
(1.00) 		0.48
(1.00) 		0.94
(1.00)
2p gain 30 (10%) 275 0.72
(1.00) 		0.92
(1.00) 		0.395
(1.00) 		0.872
(1.00) 		0.796
(1.00) 		0.542
(1.00) 		0.658
(1.00) 		0.019
(1.00) 		0.315
(1.00) 		0.148
(1.00) 		0.834
(1.00)
2q gain 20 (7%) 285 0.79
(1.00) 		0.914
(1.00) 		0.606
(1.00) 		0.832
(1.00) 		0.868
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.0838
(1.00) 		0.0665
(1.00) 		0.0558
(1.00) 		0.615
(1.00)
3p gain 27 (9%) 278 0.276
(1.00) 		0.524
(1.00) 		0.368
(1.00) 		0.872
(1.00) 		0.654
(1.00) 		0.919
(1.00) 		0.641
(1.00) 		0.0928
(1.00) 		0.186
(1.00) 		0.127
(1.00) 		0.331
(1.00)
3q gain 102 (33%) 203 0.387
(1.00) 		0.315
(1.00) 		0.0581
(1.00) 		0.834
(1.00) 		0.637
(1.00) 		0.249
(1.00) 		0.00477
(1.00) 		0.162
(1.00) 		0.454
(1.00) 		0.983
(1.00) 		0.814
(1.00)
4p gain 13 (4%) 292 0.657
(1.00) 		0.113
(1.00) 		0.758
(1.00) 		0.858
(1.00) 		0.574
(1.00) 		0.41
(1.00) 		0.322
(1.00) 		0.556
(1.00) 		0.143
(1.00) 		0.81
(1.00) 		0.99
(1.00)
4q gain 9 (3%) 296 0.558
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.226
(1.00) 		0.581
(1.00) 		0.413
(1.00) 		1
(1.00) 		0.614
(1.00) 		0.135
(1.00) 		0.34
(1.00) 		0.51
(1.00)
5p gain 76 (25%) 229 0.603
(1.00) 		0.363
(1.00) 		0.103
(1.00) 		0.971
(1.00) 		0.954
(1.00) 		0.586
(1.00) 		0.361
(1.00) 		0.285
(1.00) 		0.515
(1.00) 		0.517
(1.00) 		0.206
(1.00)
5q gain 28 (9%) 277 0.597
(1.00) 		0.936
(1.00) 		0.513
(1.00) 		0.727
(1.00) 		0.87
(1.00) 		0.0801
(1.00) 		0.363
(1.00) 		0.101
(1.00) 		0.546
(1.00) 		0.852
(1.00) 		0.742
(1.00)
6p gain 26 (9%) 279 0.466
(1.00) 		0.105
(1.00) 		1
(1.00) 		0.804
(1.00) 		0.428
(1.00) 		0.554
(1.00) 		0.0333
(1.00) 		0.586
(1.00) 		0.479
(1.00) 		0.766
(1.00) 		0.551
(1.00)
6q gain 19 (6%) 286 0.678
(1.00) 		0.413
(1.00) 		0.791
(1.00) 		0.312
(1.00) 		0.251
(1.00) 		0.144
(1.00) 		0.052
(1.00) 		0.792
(1.00) 		0.988
(1.00) 		0.957
(1.00) 		0.369
(1.00)
7p gain 70 (23%) 235 0.303
(1.00) 		0.0661
(1.00) 		0.362
(1.00) 		0.814
(1.00) 		0.922
(1.00) 		0.842
(1.00) 		0.876
(1.00) 		0.325
(1.00) 		0.445
(1.00) 		0.731
(1.00) 		0.865
(1.00)
7q gain 44 (14%) 261 0.272
(1.00) 		0.749
(1.00) 		0.584
(1.00) 		0.525
(1.00) 		0.463
(1.00) 		0.535
(1.00) 		0.708
(1.00) 		0.0825
(1.00) 		0.411
(1.00) 		0.732
(1.00) 		0.293
(1.00)
8p gain 47 (15%) 258 0.0188
(1.00) 		0.68
(1.00) 		0.214
(1.00) 		0.245
(1.00) 		0.489
(1.00) 		0.543
(1.00) 		0.587
(1.00) 		0.797
(1.00) 		0.0144
(1.00) 		0.037
(1.00) 		0.848
(1.00)
8q gain 129 (42%) 176 0.0972
(1.00) 		0.077
(1.00) 		0.898
(1.00) 		0.136
(1.00) 		0.347
(1.00) 		0.378
(1.00) 		0.79
(1.00) 		0.677
(1.00) 		0.12
(1.00) 		0.0844
(1.00) 		0.312
(1.00)
9p gain 37 (12%) 268 0.306
(1.00) 		0.216
(1.00) 		0.168
(1.00) 		0.885
(1.00) 		0.212
(1.00) 		0.539
(1.00) 		0.69
(1.00) 		0.145
(1.00) 		0.657
(1.00) 		0.206
(1.00) 		0.722
(1.00)
9q gain 44 (14%) 261 0.464
(1.00) 		0.118
(1.00) 		0.719
(1.00) 		0.404
(1.00) 		0.816
(1.00) 		0.584
(1.00) 		0.454
(1.00) 		0.511
(1.00) 		0.534
(1.00) 		0.142
(1.00) 		0.315
(1.00)
10p gain 13 (4%) 292 0.976
(1.00) 		0.996
(1.00) 		0.526
(1.00) 		0.814
(1.00) 		0.288
(1.00) 		0.961
(1.00) 		0.743
(1.00) 		0.192
(1.00) 		0.552
(1.00) 		0.539
(1.00) 		0.302
(1.00)
10q gain 7 (2%) 298 0.101
(1.00) 		0.903
(1.00) 		0.678
(1.00) 		0.306
(1.00) 		0.666
(1.00) 		0.372
(1.00) 		0.0675
(1.00) 		0.253
(1.00) 		0.584
(1.00) 		0.872
(1.00) 		0.574
(1.00)
11p gain 16 (5%) 289 0.664
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.162
(1.00) 		0.478
(1.00) 		0.292
(1.00) 		0.557
(1.00) 		0.962
(1.00) 		0.034
(1.00) 		0.361
(1.00) 		0.723
(1.00)
11q gain 16 (5%) 289 0.739
(1.00) 		0.216
(1.00) 		0.392
(1.00) 		0.63
(1.00) 		0.932
(1.00) 		0.484
(1.00) 		0.557
(1.00) 		0.907
(1.00) 		0.00853
(1.00) 		0.0324
(1.00) 		0.876
(1.00)
12p gain 60 (20%) 245 0.188
(1.00) 		0.362
(1.00) 		0.196
(1.00) 		0.537
(1.00) 		0.661
(1.00) 		0.919
(1.00) 		0.406
(1.00) 		0.306
(1.00) 		0.244
(1.00) 		0.446
(1.00) 		0.704
(1.00)
12q gain 25 (8%) 280 0.264
(1.00) 		0.961
(1.00) 		0.0996
(1.00) 		0.85
(1.00) 		0.779
(1.00) 		0.697
(1.00) 		0.468
(1.00) 		0.225
(1.00) 		0.639
(1.00) 		0.0829
(1.00) 		0.272
(1.00)
13q gain 17 (6%) 288 0.7
(1.00) 		0.934
(1.00) 		0.788
(1.00) 		0.468
(1.00) 		0.0669
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.522
(1.00) 		0.559
(1.00) 		0.727
(1.00) 		0.805
(1.00)
14q gain 51 (17%) 254 0.814
(1.00) 		0.907
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.344
(1.00) 		0.58
(1.00) 		0.217
(1.00) 		0.176
(1.00) 		0.00758
(1.00) 		0.422
(1.00) 		0.618
(1.00)
15q gain 13 (4%) 292 0.845
(1.00) 		0.789
(1.00) 		0.758
(1.00) 		0.0535
(1.00) 		0.693
(1.00) 		0.251
(1.00) 		0.197
(1.00) 		0.198
(1.00) 		0.326
(1.00) 		0.54
(1.00) 		0.129
(1.00)
16p gain 21 (7%) 284 0.69
(1.00) 		0.004
(1.00) 		0.804
(1.00) 		0.952
(1.00) 		0.0179
(1.00) 		0.275
(1.00) 		0.611
(1.00) 		0.731
(1.00) 		0.674
(1.00) 		0.552
(1.00) 		0.356
(1.00)
16q gain 25 (8%) 280 0.834
(1.00) 		0.142
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.102
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.67
(1.00) 		0.719
(1.00) 		0.843
(1.00)
17p gain 18 (6%) 287 0.706
(1.00) 		0.781
(1.00) 		0.171
(1.00) 		0.238
(1.00) 		0.816
(1.00) 		0.321
(1.00) 		0.781
(1.00) 		0.849
(1.00) 		0.137
(1.00) 		0.563
(1.00) 		0.267
(1.00)
17q gain 20 (7%) 285 0.988
(1.00) 		0.791
(1.00) 		0.299
(1.00) 		0.0105
(1.00) 		0.121
(1.00) 		0.0968
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.787
(1.00) 		0.0264
(1.00) 		0.7
(1.00)
18q gain 20 (7%) 285 0.0437
(1.00) 		0.738
(1.00) 		0.0747
(1.00) 		0.726
(1.00) 		0.717
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.519
(1.00) 		0.264
(1.00) 		0.472
(1.00)
19p gain 11 (4%) 294 0.0337
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.643
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.893
(1.00) 		0.679
(1.00) 		0.569
(1.00)
19q gain 21 (7%) 284 0.227
(1.00) 		0.665
(1.00) 		0.804
(1.00) 		0.108
(1.00) 		0.241
(1.00) 		0.317
(1.00) 		0.611
(1.00) 		0.737
(1.00) 		0.106
(1.00) 		0.266
(1.00) 		0.82
(1.00)
20p gain 63 (21%) 242 0.123
(1.00) 		0.19
(1.00) 		0.528
(1.00) 		0.505
(1.00) 		0.204
(1.00) 		0.267
(1.00) 		0.00885
(1.00) 		0.259
(1.00) 		0.132
(1.00) 		0.433
(1.00) 		0.977
(1.00)
20q gain 68 (22%) 237 0.539
(1.00) 		0.0261
(1.00) 		0.167
(1.00) 		0.503
(1.00) 		0.427
(1.00) 		0.586
(1.00) 		0.00644
(1.00) 		0.441
(1.00) 		0.132
(1.00) 		0.287
(1.00) 		0.467
(1.00)
21q gain 8 (3%) 297 0.92
(1.00) 		0.0805
(1.00) 		1
(1.00) 		0.912
(1.00) 		0.866
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.998
(1.00) 		0.0039
(1.00) 		0.447
(1.00)
22q gain 39 (13%) 266 0.492
(1.00) 		0.166
(1.00) 		0.342
(1.00) 		0.907
(1.00) 		0.219
(1.00) 		0.933
(1.00) 		0.846
(1.00) 		0.0655
(1.00) 		0.259
(1.00) 		0.551
(1.00) 		0.321
(1.00)
Xq gain 22 (7%) 283 0.0632
(1.00) 		0.55
(1.00) 		0.805
(1.00) 		0.73
(1.00) 		0.169
(1.00) 		0.974
(1.00) 		0.611
(1.00) 		0.142
(1.00) 		0.0441
(1.00) 		0.928
(1.00) 		0.7
(1.00)
1p loss 16 (5%) 289 0.231
(1.00) 		0.101
(1.00) 		0.57
(1.00) 		0.0133
(1.00) 		0.388
(1.00) 		0.304
(1.00) 		0.241
(1.00) 		0.00567
(1.00) 		0.0116
(1.00) 		0.0675
(1.00) 		0.521
(1.00)
2p loss 6 (2%) 299 0.204
(1.00) 		0.97
(1.00) 		0.669
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.641
(1.00) 		0.822
(1.00) 		0.0158
(1.00) 		0.233
(1.00) 		0.855
(1.00)
2q loss 10 (3%) 295 0.174
(1.00) 		0.693
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.444
(1.00) 		0.142
(1.00) 		0.46
(1.00) 		0.0881
(1.00) 		0.573
(1.00) 		0.409
(1.00) 		0.842
(1.00)
3p loss 117 (38%) 188 0.00489
(1.00) 		0.918
(1.00) 		0.00824
(1.00) 		0.376
(1.00) 		0.0258
(1.00) 		0.76
(1.00) 		1
(1.00) 		0.0213
(1.00) 		0.559
(1.00) 		0.168
(1.00) 		0.0326
(1.00)
3q loss 21 (7%) 284 0.272
(1.00) 		0.396
(1.00) 		0.209
(1.00) 		0.363
(1.00) 		0.144
(1.00) 		0.279
(1.00) 		0.794
(1.00) 		0.719
(1.00) 		0.0475
(1.00) 		0.426
(1.00) 		0.217
(1.00)
4p loss 73 (24%) 232 0.118
(1.00) 		0.392
(1.00) 		0.233
(1.00) 		0.322
(1.00) 		0.597
(1.00) 		0.189
(1.00) 		1
(1.00) 		0.07
(1.00) 		0.00217
(1.00) 		0.000309
(0.268) 		0.412
(1.00)
4q loss 50 (16%) 255 0.944
(1.00) 		0.648
(1.00) 		0.864
(1.00) 		0.259
(1.00) 		0.622
(1.00) 		0.437
(1.00) 		0.594
(1.00) 		0.205
(1.00) 		0.0617
(1.00) 		0.426
(1.00) 		0.624
(1.00)
5p loss 9 (3%) 296 0.451
(1.00) 		0.0976
(1.00) 		0.266
(1.00) 		0.858
(1.00) 		0.906
(1.00) 		0.604
(1.00) 		0.119
(1.00) 		0.76
(1.00) 		0.559
(1.00) 		0.43
(1.00) 		0.22
(1.00)
5q loss 62 (20%) 243 0.281
(1.00) 		0.111
(1.00) 		0.426
(1.00) 		0.28
(1.00) 		0.596
(1.00) 		0.33
(1.00) 		1
(1.00) 		0.00584
(1.00) 		0.996
(1.00) 		0.0784
(1.00) 		0.809
(1.00)
6p loss 19 (6%) 286 0.336
(1.00) 		0.675
(1.00) 		0.297
(1.00) 		0.00143
(1.00) 		0.614
(1.00) 		0.125
(1.00) 		0.583
(1.00) 		0.236
(1.00) 		0.308
(1.00) 		0.137
(1.00) 		0.954
(1.00)
6q loss 21 (7%) 284 0.794
(1.00) 		0.167
(1.00) 		0.455
(1.00) 		0.0178
(1.00) 		0.567
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.472
(1.00) 		0.637
(1.00) 		0.784
(1.00)
7p loss 5 (2%) 300 0.78
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.712
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(1.00) 		0.16
(1.00) 		0.0326
(1.00) 		0.832
(1.00)
7q loss 9 (3%) 296 0.84
(1.00) 		0.807
(1.00) 		0.71
(1.00) 		0.277
(1.00) 		0.581
(1.00) 		0.778
(1.00) 		0.459
(1.00) 		0.437
(1.00) 		0.549
(1.00) 		0.829
(1.00) 		0.943
(1.00)
8p loss 62 (20%) 243 0.0324
(1.00) 		0.763
(1.00) 		0.753
(1.00) 		0.0124
(1.00) 		0.904
(1.00) 		0.144
(1.00) 		0.624
(1.00) 		0.0646
(1.00) 		0.716
(1.00) 		0.843
(1.00) 		0.976
(1.00)
8q loss 7 (2%) 298 0.244
(1.00) 		0.713
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.0816
(1.00) 		0.457
(1.00) 		0.469
(1.00)
9p loss 84 (28%) 221 0.331
(1.00) 		0.312
(1.00) 		0.254
(1.00) 		0.818
(1.00) 		0.949
(1.00) 		0.535
(1.00) 		1
(1.00) 		0.00831
(1.00) 		0.0158
(1.00) 		0.0153
(1.00) 		0.896
(1.00)
9q loss 29 (10%) 276 0.422
(1.00) 		0.311
(1.00) 		1
(1.00) 		0.894
(1.00) 		0.804
(1.00) 		0.305
(1.00) 		0.821
(1.00) 		0.0836
(1.00) 		0.737
(1.00) 		0.209
(1.00) 		0.608
(1.00)
10p loss 44 (14%) 261 0.269
(1.00) 		0.346
(1.00) 		0.28
(1.00) 		0.0628
(1.00) 		0.587
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.0776
(1.00) 		0.303
(1.00) 		0.359
(1.00) 		0.791
(1.00)
10q loss 25 (8%) 280 0.384
(1.00) 		0.593
(1.00) 		0.0996
(1.00) 		0.305
(1.00) 		0.803
(1.00) 		0.371
(1.00) 		0.809
(1.00) 		0.515
(1.00) 		0.45
(1.00) 		0.265
(1.00) 		0.176
(1.00)
11p loss 38 (12%) 267 0.368
(1.00) 		0.93
(1.00) 		0.438
(1.00) 		0.78
(1.00) 		0.0327
(1.00) 		0.124
(1.00) 		0.55
(1.00) 		0.339
(1.00) 		0.022
(1.00) 		0.0675
(1.00) 		0.789
(1.00)
11q loss 58 (19%) 247 0.763
(1.00) 		0.437
(1.00) 		0.0226
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.533
(1.00) 		0.0418
(1.00) 		0.692
(1.00) 		0.835
(1.00) 		0.616
(1.00) 		0.308
(1.00)
12p loss 11 (4%) 294 0.125
(1.00) 		0.00969
(1.00) 		0.3
(1.00) 		0.068
(1.00) 		0.0293
(1.00) 		0.125
(1.00) 		0.0312
(1.00) 		0.129
(1.00) 		0.636
(1.00) 		0.484
(1.00) 		0.00676
(1.00)
12q loss 8 (3%) 297 0.645
(1.00) 		0.406
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.624
(1.00) 		0.478
(1.00) 		0.427
(1.00)
13q loss 60 (20%) 245 0.706
(1.00) 		0.527
(1.00) 		0.0368
(1.00) 		0.601
(1.00) 		0.718
(1.00) 		0.32
(1.00) 		0.618
(1.00) 		0.0928
(1.00) 		0.424
(1.00) 		0.111
(1.00) 		0.344
(1.00)
14q loss 14 (5%) 291 0.711
(1.00) 		0.997
(1.00) 		0.364
(1.00) 		0.232
(1.00) 		0.723
(1.00) 		0.289
(1.00) 		0.349
(1.00) 		0.665
(1.00) 		0.603
(1.00) 		0.929
(1.00) 		0.619
(1.00)
15q loss 23 (8%) 282 0.561
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.456
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.00124
(1.00) 		0.502
(1.00) 		0.767
(1.00)
16p loss 10 (3%) 295 0.267
(1.00) 		0.574
(1.00) 		0.733
(1.00) 		0.586
(1.00) 		0.39
(1.00) 		0.812
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.349
(1.00) 		0.0634
(1.00) 		0.135
(1.00)
16q loss 23 (8%) 282 0.307
(1.00) 		0.927
(1.00) 		0.145
(1.00) 		0.744
(1.00) 		0.874
(1.00) 		0.552
(1.00) 		0.462
(1.00) 		0.435
(1.00) 		0.724
(1.00) 		0.387
(1.00) 		0.426
(1.00)
17p loss 43 (14%) 262 0.544
(1.00) 		0.0534
(1.00) 		0.0965
(1.00) 		0.173
(1.00) 		0.74
(1.00) 		0.101
(1.00) 		0.347
(1.00) 		0.289
(1.00) 		0.322
(1.00) 		0.3
(1.00) 		0.328
(1.00)
17q loss 5 (2%) 300 0.703
(1.00) 		0.528
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.431
(1.00) 		0.101
(1.00) 		0.345
(1.00) 		0.00225
(1.00) 		0.503
(1.00) 		0.666
(1.00)
18p loss 28 (9%) 277 0.699
(1.00) 		0.535
(1.00) 		0.657
(1.00) 		0.847
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.649
(1.00) 		0.727
(1.00) 		0.193
(1.00) 		0.777
(1.00) 		0.318
(1.00)
18q loss 82 (27%) 223 0.0769
(1.00) 		0.0448
(1.00) 		0.316
(1.00) 		0.755
(1.00) 		0.353
(1.00) 		0.708
(1.00) 		0.882
(1.00) 		0.175
(1.00) 		0.0028
(1.00) 		0.104
(1.00) 		0.21
(1.00)
19p loss 26 (9%) 279 0.01
(1.00) 		0.743
(1.00) 		0.0198
(1.00) 		0.17
(1.00) 		0.106
(1.00) 		0.0757
(1.00) 		0.637
(1.00) 		0.145
(1.00) 		0.421
(1.00) 		0.364
(1.00) 		0.105
(1.00)
19q loss 19 (6%) 286 0.0567
(1.00) 		0.49
(1.00) 		0.112
(1.00) 		0.00758
(1.00) 		0.13
(1.00) 		0.0219
(1.00) 		1
(1.00) 		0.164
(1.00) 		0.00146
(1.00) 		0.0341
(1.00) 		0.554
(1.00)
20p loss 21 (7%) 284 0.705
(1.00) 		0.117
(1.00) 		0.209
(1.00) 		0.536
(1.00) 		0.294
(1.00) 		0.486
(1.00) 		0.611
(1.00) 		0.677
(1.00) 		0.298
(1.00) 		0.278
(1.00) 		0.219
(1.00)
20q loss 10 (3%) 295 0.261
(1.00) 		0.508
(1.00) 		0.067
(1.00) 		0.293
(1.00) 		0.734
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.97
(1.00) 		0.695
(1.00) 		0.459
(1.00)
21q loss 53 (17%) 252 0.75
(1.00) 		0.0797
(1.00) 		0.0638
(1.00) 		0.346
(1.00) 		0.00994
(1.00) 		1
(1.00) 		1
(1.00) 		0.095
(1.00) 		0.181
(1.00) 		0.927
(1.00) 		0.659
(1.00)
22q loss 24 (8%) 281 0.172
(1.00) 		0.957
(1.00) 		0.245
(1.00) 		0.468
(1.00) 		0.166
(1.00) 		0.259
(1.00) 		0.807
(1.00) 		0.341
(1.00) 		0.719
(1.00) 		0.623
(1.00) 		0.49
(1.00)
Xq loss 9 (3%) 296 0.541
(1.00) 		0.828
(1.00) 		0.121
(1.00) 		0.34
(1.00) 		0.0907
(1.00) 		0.0407
(1.00) 		0.695
(1.00) 		0.381
(1.00) 		0.313
(1.00) 		0.547
(1.00) 		0.619
(1.00)
'18p gain mutation analysis' versus 'GENDER'

P value = 0.000263 (Fisher's exact test), Q value = 0.23

Table S1.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 84 221
18P GAIN MUTATED 4 47
18P GAIN WILD-TYPE 80 174

Figure S1.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'GENDER'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = HNSC-TP.clin.merged.picked.txt

  • Number of patients = 305

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 11

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

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] 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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