Correlation between copy number variations of arm-level result and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1XG9P6N
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1XG9P6N
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 325 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 RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test Chi-square test t-test t-test Chi-square test
18p gain 0 (0%) 271 0.201
(1.00) 		0.391
(1.00) 		9.89e-05
(0.0776) 		0.383
(1.00) 		0.245
(1.00) 		0.698
(1.00) 		0.477
(1.00) 		0.463
(1.00) 		0.476
(1.00) 		0.108
(1.00)
1p gain 0 (0%) 314 0.826
(1.00) 		0.555
(1.00) 		0.0797
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.953
(1.00) 		0.656
(1.00) 		0.667
(1.00) 		0.819
(1.00)
1q gain 0 (0%) 286 0.829
(1.00) 		0.992
(1.00) 		0.705
(1.00) 		0.163
(1.00) 		0.975
(1.00) 		0.744
(1.00) 		0.366
(1.00) 		0.0659
(1.00) 		0.113
(1.00) 		0.126
(1.00)
2p gain 0 (0%) 294 0.72
(1.00) 		0.986
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.0217
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.503
(1.00) 		0.818
(1.00)
2q gain 0 (0%) 303 0.687
(1.00) 		0.694
(1.00) 		0.337
(1.00) 		0.437
(1.00) 		0.0407
(1.00) 		0.807
(1.00) 		1
(1.00) 		0.212
(1.00) 		0.417
(1.00) 		0.954
(1.00)
3p gain 0 (0%) 298 0.2
(1.00) 		0.639
(1.00) 		0.37
(1.00) 		0.244
(1.00) 		0.138
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.971
(1.00) 		0.283
(1.00) 		0.926
(1.00)
3q gain 0 (0%) 218 0.289
(1.00) 		0.477
(1.00) 		0.0185
(1.00) 		0.000894
(0.7) 		0.175
(1.00) 		0.526
(1.00) 		1
(1.00) 		0.834
(1.00) 		0.515
(1.00) 		0.198
(1.00)
4p gain 0 (0%) 312 0.698
(1.00) 		0.116
(1.00) 		0.761
(1.00) 		0.316
(1.00) 		0.55
(1.00) 		0.82
(1.00) 		0.279
(1.00) 		0.411
(1.00) 		0.308
(1.00)
4q gain 0 (0%) 316 0.528
(1.00) 		0.774
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.415
(1.00) 		0.55
(1.00) 		0.407
(1.00) 		0.279
(1.00)
5p gain 0 (0%) 243 0.725
(1.00) 		0.312
(1.00) 		0.0638
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.14
(1.00) 		0.0159
(1.00) 		0.695
(1.00) 		0.107
(1.00) 		0.473
(1.00)
5q gain 0 (0%) 295 0.647
(1.00) 		0.97
(1.00) 		0.672
(1.00) 		0.26
(1.00) 		0.049
(1.00) 		0.683
(1.00) 		0.303
(1.00) 		0.0935
(1.00) 		0.0393
(1.00) 		0.113
(1.00)
6p gain 0 (0%) 299 0.515
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.0531
(1.00) 		0.599
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.39
(1.00) 		0.833
(1.00) 		0.612
(1.00)
6q gain 0 (0%) 306 0.625
(1.00) 		0.423
(1.00) 		0.793
(1.00) 		0.0531
(1.00) 		0.8
(1.00) 		0.481
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.821
(1.00) 		0.174
(1.00)
7p gain 0 (0%) 252 0.497
(1.00) 		0.119
(1.00) 		0.554
(1.00) 		0.877
(1.00) 		0.572
(1.00) 		0.741
(1.00) 		0.301
(1.00) 		0.224
(1.00) 		0.632
(1.00) 		0.921
(1.00)
7q gain 0 (0%) 280 0.453
(1.00) 		0.535
(1.00) 		0.474
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.447
(1.00) 		0.366
(1.00) 		0.68
(1.00) 		0.591
(1.00) 		0.54
(1.00)
8p gain 0 (0%) 276 0.0192
(1.00) 		0.481
(1.00) 		0.121
(1.00) 		0.858
(1.00) 		0.788
(1.00) 		0.832
(1.00) 		0.526
(1.00) 		0.307
(1.00) 		0.526
(1.00) 		0.274
(1.00)
8q gain 0 (0%) 191 0.241
(1.00) 		0.0436
(1.00) 		0.802
(1.00) 		0.793
(1.00) 		0.501
(1.00) 		0.281
(1.00) 		0.175
(1.00) 		0.48
(1.00) 		0.512
(1.00) 		0.608
(1.00)
9p gain 0 (0%) 286 0.273
(1.00) 		0.284
(1.00) 		0.0593
(1.00) 		0.427
(1.00) 		0.0393
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.449
(1.00) 		0.264
(1.00)
9q gain 0 (0%) 275 0.459
(1.00) 		0.252
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.732
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.492
(1.00) 		0.669
(1.00)
10p gain 0 (0%) 313 0.963
(1.00) 		0.712
(1.00) 		0.521
(1.00) 		0.491
(1.00) 		0.384
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.821
(1.00) 		0.0211
(1.00) 		0.864
(1.00)
10q gain 0 (0%) 319 0.0669
(1.00) 		0.49
(1.00) 		1
(1.00) 		0.0312
(1.00) 		0.509
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.975
(1.00) 		0.827
(1.00) 		0.727
(1.00)
11p gain 0 (0%) 309 0.701
(1.00) 		0.175
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.955
(1.00) 		0.862
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.368
(1.00) 		0.322
(1.00)
11q gain 0 (0%) 309 0.699
(1.00) 		0.221
(1.00) 		0.398
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.742
(1.00) 		1
(1.00) 		0.968
(1.00) 		0.0623
(1.00) 		0.787
(1.00)
12p gain 0 (0%) 263 0.233
(1.00) 		0.204
(1.00) 		0.0584
(1.00) 		0.621
(1.00) 		0.413
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.565
(1.00) 		0.775
(1.00) 		0.89
(1.00)
12q gain 0 (0%) 301 0.294
(1.00) 		0.861
(1.00) 		0.0985
(1.00) 		0.134
(1.00) 		0.214
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.609
(1.00) 		0.799
(1.00)
13q gain 0 (0%) 307 0.75
(1.00) 		0.696
(1.00) 		1
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.474
(1.00) 		1
(1.00) 		0.205
(1.00) 		0.488
(1.00) 		0.457
(1.00)
14q gain 0 (0%) 271 0.819
(1.00) 		0.848
(1.00) 		0.512
(1.00) 		0.221
(1.00) 		0.233
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.644
(1.00) 		0.597
(1.00) 		0.141
(1.00)
15q gain 0 (0%) 313 0.803
(1.00) 		0.797
(1.00) 		0.745
(1.00) 		0.306
(1.00) 		0.177
(1.00) 		0.0968
(1.00) 		1
(1.00) 		0.0417
(1.00) 		0.503
(1.00) 		0.944
(1.00)
16p gain 0 (0%) 303 0.726
(1.00) 		0.00268
(1.00) 		0.806
(1.00) 		0.613
(1.00) 		0.808
(1.00) 		0.346
(1.00) 		1
(1.00) 		0.0543
(1.00) 		0.0177
(1.00) 		0.0423
(1.00)
16q gain 0 (0%) 296 0.777
(1.00) 		0.0571
(1.00) 		0.829
(1.00) 		0.821
(1.00) 		0.219
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.8
(1.00) 		0.13
(1.00)
17p gain 0 (0%) 307 0.479
(1.00) 		0.629
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.939
(1.00) 		0.545
(1.00) 		0.303
(1.00) 		0.23
(1.00) 		0.496
(1.00) 		0.252
(1.00)
17q gain 0 (0%) 303 0.732
(1.00) 		0.863
(1.00) 		0.145
(1.00) 		0.613
(1.00) 		0.397
(1.00) 		0.9
(1.00) 		0.104
(1.00) 		0.0831
(1.00) 		0.47
(1.00) 		0.206
(1.00)
18q gain 0 (0%) 305 0.052
(1.00) 		0.756
(1.00) 		0.0185
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.614
(1.00) 		0.67
(1.00) 		0.743
(1.00)
19p gain 0 (0%) 313 0.0282
(1.00) 		0.0751
(1.00) 		1
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.452
(1.00) 		0.236
(1.00) 		0.842
(1.00) 		0.37
(1.00) 		0.675
(1.00)
19q gain 0 (0%) 304 0.258
(1.00) 		0.681
(1.00) 		0.804
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.918
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.794
(1.00) 		0.255
(1.00)
20p gain 0 (0%) 259 0.154
(1.00) 		0.163
(1.00) 		0.357
(1.00) 		0.00558
(1.00) 		0.328
(1.00) 		0.848
(1.00) 		0.591
(1.00) 		0.41
(1.00) 		0.408
(1.00) 		0.398
(1.00)
20q gain 0 (0%) 255 0.633
(1.00) 		0.0217
(1.00) 		0.1
(1.00) 		0.00673
(1.00) 		0.415
(1.00) 		0.677
(1.00) 		0.581
(1.00) 		0.493
(1.00) 		0.888
(1.00) 		0.629
(1.00)
21q gain 0 (0%) 316 0.951
(1.00) 		0.111
(1.00) 		1
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.96
(1.00) 		0.481
(1.00) 		0.235
(1.00)
22q gain 0 (0%) 285 0.432
(1.00) 		0.279
(1.00) 		0.264
(1.00) 		0.558
(1.00) 		0.106
(1.00) 		0.416
(1.00) 		0.571
(1.00) 		0.109
(1.00) 		0.673
(1.00) 		0.695
(1.00)
Xq gain 0 (0%) 305 0.0176
(1.00) 		0.584
(1.00) 		0.21
(1.00) 		0.792
(1.00) 		0.197
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.0589
(1.00) 		0.136
(1.00) 		0.72
(1.00)
1p loss 0 (0%) 309 0.208
(1.00) 		0.0967
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.00602
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.336
(1.00) 		0.398
(1.00)
2p loss 0 (0%) 321 0.329
(1.00) 		0.809
(1.00) 		0.313
(1.00) 		0.244
(1.00) 		0.552
(1.00) 		0.81
(1.00) 		0.936
(1.00) 		0.0153
(1.00) 		0.957
(1.00)
2q loss 0 (0%) 316 0.254
(1.00) 		0.707
(1.00) 		0.714
(1.00) 		0.692
(1.00) 		0.138
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.275
(1.00) 		0.494
(1.00) 		0.135
(1.00)
3p loss 0 (0%) 202 0.00766
(1.00) 		0.557
(1.00) 		0.00347
(1.00) 		0.592
(1.00) 		0.0613
(1.00) 		0.0641
(1.00) 		0.104
(1.00) 		0.263
(1.00) 		0.215
(1.00) 		0.24
(1.00)
3q loss 0 (0%) 306 0.451
(1.00) 		0.436
(1.00) 		0.297
(1.00) 		0.58
(1.00) 		0.732
(1.00) 		0.352
(1.00) 		1
(1.00) 		0.208
(1.00) 		0.128
(1.00) 		0.368
(1.00)
4p loss 0 (0%) 247 0.113
(1.00) 		0.336
(1.00) 		0.0596
(1.00) 		0.45
(1.00) 		0.137
(1.00) 		0.477
(1.00) 		0.231
(1.00) 		0.394
(1.00) 		0.0954
(1.00) 		0.208
(1.00)
4q loss 0 (0%) 275 0.758
(1.00) 		0.382
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.457
(1.00) 		0.366
(1.00) 		0.73
(1.00) 		0.212
(1.00) 		0.483
(1.00)
5p loss 0 (0%) 317 0.944
(1.00) 		0.0596
(1.00) 		0.691
(1.00) 		0.206
(1.00) 		0.762
(1.00) 		0.292
(1.00) 		1
(1.00) 		0.941
(1.00) 		0.389
(1.00) 		0.568
(1.00)
5q loss 0 (0%) 262 0.444
(1.00) 		0.267
(1.00) 		0.0867
(1.00) 		0.745
(1.00) 		0.00626
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.409
(1.00) 		0.628
(1.00) 		0.19
(1.00)
6p loss 0 (0%) 306 0.306
(1.00) 		0.69
(1.00) 		0.297
(1.00) 		0.414
(1.00) 		0.246
(1.00) 		0.681
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.553
(1.00) 		0.18
(1.00)
6q loss 0 (0%) 304 0.848
(1.00) 		0.174
(1.00) 		0.455
(1.00) 		0.602
(1.00) 		0.816
(1.00) 		0.502
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.183
(1.00) 		0.193
(1.00)
7p loss 0 (0%) 320 0.807
(1.00) 		0.49
(1.00) 		1
(1.00) 		1
(1.00) 		0.233
(1.00) 		0.712
(1.00) 		0.732
(1.00) 		0.521
(1.00) 		0.827
(1.00)
7q loss 0 (0%) 316 0.809
(1.00) 		0.816
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.324
(1.00) 		0.514
(1.00)
8p loss 0 (0%) 254 0.0901
(1.00) 		0.961
(1.00) 		0.766
(1.00) 		0.755
(1.00) 		0.271
(1.00) 		0.487
(1.00) 		0.144
(1.00) 		0.68
(1.00) 		0.271
(1.00) 		0.102
(1.00)
8q loss 0 (0%) 319 0.0567
(1.00) 		0.754
(1.00) 		0.191
(1.00) 		0.633
(1.00) 		0.204
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.7
(1.00) 		0.561
(1.00)
9p loss 0 (0%) 234 0.552
(1.00) 		0.565
(1.00) 		0.271
(1.00) 		0.885
(1.00) 		0.0275
(1.00) 		0.993
(1.00) 		0.6
(1.00) 		0.702
(1.00) 		0.953
(1.00) 		0.235
(1.00)
9q loss 0 (0%) 294 0.386
(1.00) 		0.471
(1.00) 		0.674
(1.00) 		0.509
(1.00) 		0.104
(1.00) 		0.541
(1.00) 		0.423
(1.00) 		0.404
(1.00) 		0.174
(1.00) 		0.503
(1.00)
10p loss 0 (0%) 277 0.223
(1.00) 		0.526
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.0591
(1.00) 		0.722
(1.00) 		0.0772
(1.00) 		0.737
(1.00) 		0.757
(1.00) 		0.288
(1.00)
10q loss 0 (0%) 299 0.416
(1.00) 		0.943
(1.00) 		0.0667
(1.00) 		0.472
(1.00) 		0.509
(1.00) 		0.103
(1.00) 		0.366
(1.00) 		0.966
(1.00) 		0.157
(1.00) 		0.456
(1.00)
11p loss 0 (0%) 282 0.336
(1.00) 		0.908
(1.00) 		0.362
(1.00) 		0.566
(1.00) 		0.551
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.0195
(1.00) 		0.496
(1.00) 		0.00951
(1.00)
11q loss 0 (0%) 263 0.682
(1.00) 		0.342
(1.00) 		0.00761
(1.00) 		0.0484
(1.00) 		0.841
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.263
(1.00) 		0.166
(1.00)
12p loss 0 (0%) 314 0.0984
(1.00) 		0.0128
(1.00) 		0.303
(1.00) 		0.142
(1.00) 		0.145
(1.00) 		0.0094
(1.00) 		0.0248
(1.00) 		0.7
(1.00) 		0.096
(1.00)
12q loss 0 (0%) 318 0.706
(1.00) 		0.418
(1.00) 		0.678
(1.00) 		0.675
(1.00) 		0.615
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.866
(1.00) 		0.802
(1.00) 		0.74
(1.00)
13q loss 0 (0%) 262 0.544
(1.00) 		0.146
(1.00) 		0.0423
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.197
(1.00) 		0.6
(1.00) 		0.71
(1.00) 		0.914
(1.00) 		0.932
(1.00)
14q loss 0 (0%) 309 0.67
(1.00) 		0.89
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.0572
(1.00) 		0.202
(1.00)
15q loss 0 (0%) 301 0.337
(1.00) 		0.794
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.0932
(1.00) 		0.287
(1.00) 		0.109
(1.00)
16p loss 0 (0%) 313 0.404
(1.00) 		0.273
(1.00) 		0.521
(1.00) 		0.738
(1.00) 		0.412
(1.00) 		0.0972
(1.00) 		0.163
(1.00) 		0.74
(1.00) 		0.746
(1.00) 		0.522
(1.00)
16q loss 0 (0%) 300 0.276
(1.00) 		0.581
(1.00) 		0.0672
(1.00) 		1
(1.00) 		0.43
(1.00) 		0.305
(1.00) 		0.236
(1.00) 		0.213
(1.00) 		0.333
(1.00) 		0.63
(1.00)
17p loss 0 (0%) 280 0.483
(1.00) 		0.0436
(1.00) 		0.11
(1.00) 		0.852
(1.00) 		0.363
(1.00) 		0.328
(1.00) 		0.477
(1.00) 		0.94
(1.00) 		0.572
(1.00) 		0.0948
(1.00)
17q loss 0 (0%) 320 0.603
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.0916
(1.00) 		0.39
(1.00) 		0.493
(1.00) 		0.0845
(1.00) 		0.881
(1.00) 		0.00118
(0.924) 		0.849
(1.00)
18p loss 0 (0%) 296 0.787
(1.00) 		0.43
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.47
(1.00) 		1
(1.00) 		0.75
(1.00) 		0.349
(1.00) 		0.894
(1.00)
18q loss 0 (0%) 235 0.115
(1.00) 		0.103
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.113
(1.00) 		0.166
(1.00) 		0.363
(1.00) 		0.524
(1.00) 		0.67
(1.00)
19p loss 0 (0%) 297 0.00787
(1.00) 		0.884
(1.00) 		0.0451
(1.00) 		0.497
(1.00) 		0.157
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.764
(1.00) 		0.024
(1.00)
19q loss 0 (0%) 304 0.0458
(1.00) 		0.735
(1.00) 		0.209
(1.00) 		0.428
(1.00) 		0.205
(1.00) 		0.502
(1.00) 		1
(1.00) 		0.0679
(1.00) 		0.641
(1.00) 		0.00214
(1.00)
20p loss 0 (0%) 304 0.847
(1.00) 		0.395
(1.00) 		0.209
(1.00) 		0.793
(1.00) 		0.509
(1.00) 		0.387
(1.00) 		0.303
(1.00) 		0.804
(1.00) 		0.405
(1.00) 		0.434
(1.00)
20q loss 0 (0%) 315 0.158
(1.00) 		0.748
(1.00) 		0.0674
(1.00) 		1
(1.00) 		0.362
(1.00) 		0.231
(1.00) 		0.163
(1.00) 		0.702
(1.00) 		0.455
(1.00) 		0.561
(1.00)
21q loss 0 (0%) 267 0.996
(1.00) 		0.277
(1.00) 		0.0524
(1.00) 		0.397
(1.00) 		0.15
(1.00) 		0.659
(1.00) 		0.164
(1.00) 		0.0394
(1.00) 		0.864
(1.00) 		0.0334
(1.00)
22q loss 0 (0%) 300 0.156
(1.00) 		0.918
(1.00) 		0.245
(1.00) 		0.465
(1.00) 		0.369
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.00343
(1.00) 		0.308
(1.00)
Xq loss 0 (0%) 318 0.355
(1.00) 		0.987
(1.00) 		0.0992
(1.00) 		0.675
(1.00) 		0.301
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.409
(1.00) 		0.0633
(1.00) 		0.62
(1.00)
'18p gain' versus 'GENDER'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.078

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

nPatients FEMALE MALE
ALL 91 234
18P GAIN CNV 4 50
18P GAIN WILD-TYPE 87 184

Figure S1.  Get High-res Image Gene #32: '18p gain' 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 = 325

  • 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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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