Correlation between copy number variation genes (focal events) and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1VM4BQ3
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 54 focal events and 14 clinical features across 367 patients, 4 significant findings detected with Q value < 0.25.

  • amp_3p13 cnv correlated to 'Time from Specimen Diagnosis to Death'.

  • amp_6q12 cnv correlated to 'PATHOLOGIC_STAGE'.

  • del_10q26.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_11p15.5 cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 54 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 significant findings detected.

Clinical
Features
Time
from
Specimen
Diagnosis
to
Death
Time
to
Death
YEARS
TO
BIRTH
PATHOLOGIC
STAGE
PATHOLOGY
T
STAGE
PATHOLOGY
N
STAGE
PATHOLOGY
M
STAGE
MELANOMA
ULCERATION
MELANOMA
PRIMARY
KNOWN
BRESLOW
THICKNESS
GENDER RADIATION
THERAPY
RACE ETHNICITY
nCNV (%) nWild-Type logrank test logrank test Wilcoxon-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 Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3p13 103 (28%) 264 0.00025
(0.0946)
0.00302
(0.367)
0.247
(0.959)
0.508
(0.978)
0.481
(0.968)
0.451
(0.966)
0.46
(0.966)
1
(1.00)
0.301
(0.959)
0.382
(0.962)
0.0551
(0.935)
0.224
(0.959)
0.73
(1.00)
0.197
(0.959)
amp 6q12 81 (22%) 286 0.129
(0.959)
0.576
(0.99)
0.231
(0.959)
0.00116
(0.219)
0.383
(0.962)
0.322
(0.962)
0.00625
(0.547)
0.337
(0.962)
0.851
(1.00)
0.746
(1.00)
0.299
(0.959)
0.851
(1.00)
0.451
(0.966)
1
(1.00)
del 10q26 3 236 (64%) 131 0.234
(0.959)
0.164
(0.959)
0.00018
(0.0946)
0.361
(0.962)
0.208
(0.959)
0.298
(0.959)
0.251
(0.959)
0.78
(1.00)
0.515
(0.978)
0.181
(0.959)
0.116
(0.949)
0.872
(1.00)
0.0241
(0.792)
0.703
(1.00)
del 11p15 5 114 (31%) 253 0.798
(1.00)
0.575
(0.99)
0.101
(0.949)
0.456
(0.966)
0.223
(0.959)
0.375
(0.962)
0.814
(1.00)
0.112
(0.949)
0.243
(0.959)
0.179
(0.959)
0.000691
(0.174)
0.242
(0.959)
1
(1.00)
0.103
(0.949)
amp 1p12 121 (33%) 246 0.454
(0.966)
0.114
(0.949)
0.436
(0.966)
0.112
(0.949)
0.476
(0.968)
0.683
(1.00)
0.647
(1.00)
0.667
(1.00)
0.74
(1.00)
0.565
(0.99)
0.647
(1.00)
0.0193
(0.792)
0.772
(1.00)
0.689
(1.00)
amp 1q21 3 203 (55%) 164 0.881
(1.00)
0.606
(1.00)
0.349
(0.962)
0.439
(0.966)
1
(1.00)
0.415
(0.966)
0.514
(0.978)
0.783
(1.00)
0.534
(0.978)
0.951
(1.00)
0.746
(1.00)
0.638
(1.00)
0.813
(1.00)
0.47
(0.968)
amp 1q44 201 (55%) 166 0.308
(0.959)
0.213
(0.959)
0.828
(1.00)
0.698
(1.00)
0.574
(0.99)
0.761
(1.00)
1
(1.00)
0.412
(0.966)
0.876
(1.00)
0.473
(0.968)
0.829
(1.00)
0.533
(0.978)
0.816
(1.00)
0.466
(0.968)
amp 4q12 65 (18%) 302 0.118
(0.949)
0.312
(0.959)
0.266
(0.959)
0.189
(0.959)
0.232
(0.959)
0.503
(0.978)
0.391
(0.966)
0.483
(0.968)
0.686
(1.00)
0.582
(0.99)
0.674
(1.00)
0.838
(1.00)
1
(1.00)
0.615
(1.00)
amp 5p15 33 110 (30%) 257 0.371
(0.962)
0.722
(1.00)
0.909
(1.00)
0.821
(1.00)
0.24
(0.959)
0.0449
(0.935)
1
(1.00)
1
(1.00)
0.501
(0.978)
0.768
(1.00)
1
(1.00)
0.735
(1.00)
0.305
(0.959)
0.438
(0.966)
amp 5q35 3 59 (16%) 308 0.972
(1.00)
0.77
(1.00)
0.19
(0.959)
0.856
(1.00)
0.705
(1.00)
0.119
(0.949)
0.231
(0.959)
0.583
(0.99)
0.833
(1.00)
0.509
(0.978)
0.305
(0.959)
0.527
(0.978)
0.649
(1.00)
0.0906
(0.949)
amp 6p24 3 211 (57%) 156 0.0865
(0.949)
0.0331
(0.935)
0.0157
(0.789)
0.175
(0.959)
0.0817
(0.949)
0.946
(1.00)
0.828
(1.00)
0.407
(0.966)
0.875
(1.00)
0.0921
(0.949)
0.447
(0.966)
0.154
(0.959)
1
(1.00)
1
(1.00)
amp 7p22 1 209 (57%) 158 0.0389
(0.935)
0.428
(0.966)
0.989
(1.00)
0.105
(0.949)
0.264
(0.959)
0.32
(0.962)
0.657
(1.00)
0.682
(1.00)
0.115
(0.949)
0.906
(1.00)
1
(1.00)
1
(1.00)
0.04
(0.935)
0.704
(1.00)
amp 7q34 225 (61%) 142 0.103
(0.949)
0.335
(0.962)
0.262
(0.959)
0.0128
(0.69)
0.223
(0.959)
0.385
(0.962)
0.822
(1.00)
0.399
(0.966)
0.525
(0.978)
0.581
(0.99)
0.0766
(0.949)
0.526
(0.978)
0.352
(0.962)
1
(1.00)
amp 8q24 21 192 (52%) 175 0.0606
(0.935)
0.26
(0.959)
0.168
(0.959)
0.0667
(0.938)
0.35
(0.962)
0.321
(0.962)
0.828
(1.00)
1
(1.00)
0.532
(0.978)
0.179
(0.959)
0.518
(0.978)
0.437
(0.966)
0.0435
(0.935)
1
(1.00)
amp 11q13 3 69 (19%) 298 0.485
(0.968)
0.456
(0.966)
0.423
(0.966)
0.171
(0.959)
0.106
(0.949)
0.16
(0.959)
0.0929
(0.949)
0.862
(1.00)
0.843
(1.00)
0.589
(0.995)
0.583
(0.99)
0.111
(0.949)
0.0791
(0.949)
1
(1.00)
amp 12q14 1 58 (16%) 309 0.0499
(0.935)
0.0639
(0.938)
0.113
(0.949)
0.349
(0.962)
0.178
(0.959)
0.279
(0.959)
1
(1.00)
0.594
(0.998)
0.198
(0.959)
0.205
(0.959)
1
(1.00)
1
(1.00)
0.31
(0.959)
0.308
(0.959)
amp 12q15 59 (16%) 308 0.115
(0.949)
0.445
(0.966)
0.0737
(0.949)
0.806
(1.00)
0.384
(0.962)
0.37
(0.962)
1
(1.00)
1
(1.00)
0.199
(0.959)
0.992
(1.00)
0.382
(0.962)
0.2
(0.959)
0.658
(1.00)
0.316
(0.959)
amp 13q31 3 104 (28%) 263 0.00272
(0.367)
0.0239
(0.792)
0.974
(1.00)
0.297
(0.959)
0.0813
(0.949)
0.491
(0.968)
0.459
(0.966)
0.442
(0.966)
0.604
(1.00)
0.993
(1.00)
0.812
(1.00)
0.49
(0.968)
0.733
(1.00)
0.678
(1.00)
amp 15q26 2 120 (33%) 247 0.21
(0.959)
0.615
(1.00)
0.905
(1.00)
0.023
(0.792)
0.532
(0.978)
0.77
(1.00)
0.162
(0.959)
0.183
(0.959)
0.407
(0.966)
0.419
(0.966)
0.566
(0.99)
0.408
(0.966)
0.775
(1.00)
1
(1.00)
amp 17q25 3 122 (33%) 245 0.908
(1.00)
0.764
(1.00)
0.0034
(0.367)
0.815
(1.00)
0.158
(0.959)
0.681
(1.00)
0.82
(1.00)
0.312
(0.959)
1
(1.00)
0.903
(1.00)
0.137
(0.959)
0.741
(1.00)
0.567
(0.99)
0.432
(0.966)
amp 20q13 33 188 (51%) 179 0.0668
(0.938)
0.376
(0.962)
0.144
(0.959)
0.287
(0.959)
0.0683
(0.938)
0.697
(1.00)
0.185
(0.959)
0.136
(0.959)
0.757
(1.00)
0.155
(0.959)
1
(1.00)
1
(1.00)
0.52
(0.978)
1
(1.00)
amp 22q13 2 152 (41%) 215 0.86
(1.00)
0.527
(0.978)
0.203
(0.959)
0.567
(0.99)
0.599
(1.00)
0.305
(0.959)
1
(1.00)
0.584
(0.99)
1
(1.00)
0.763
(1.00)
0.444
(0.966)
0.875
(1.00)
0.369
(0.962)
0.247
(0.959)
del 1p36 31 81 (22%) 286 0.251
(0.959)
0.661
(1.00)
0.255
(0.959)
0.13
(0.959)
0.293
(0.959)
0.872
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.238
(0.959)
0.245
(0.959)
0.571
(0.99)
1
(1.00)
1
(1.00)
del 1p22 1 97 (26%) 270 0.387
(0.962)
0.615
(1.00)
0.15
(0.959)
0.0075
(0.567)
0.613
(1.00)
0.159
(0.959)
0.458
(0.966)
0.045
(0.935)
0.48
(0.968)
0.238
(0.959)
0.0388
(0.935)
0.48
(0.968)
0.709
(1.00)
1
(1.00)
del 2q37 3 93 (25%) 274 0.249
(0.959)
0.617
(1.00)
0.97
(1.00)
0.816
(1.00)
0.148
(0.959)
0.718
(1.00)
0.192
(0.959)
0.541
(0.985)
0.105
(0.949)
0.173
(0.959)
1
(1.00)
0.0749
(0.949)
1
(1.00)
0.0116
(0.69)
del 3p25 1 71 (19%) 296 0.3
(0.959)
0.392
(0.966)
0.258
(0.959)
0.267
(0.959)
0.387
(0.962)
0.535
(0.978)
0.391
(0.966)
0.594
(0.998)
1
(1.00)
0.0463
(0.935)
0.275
(0.959)
0.692
(1.00)
0.399
(0.966)
1
(1.00)
del 3q13 31 62 (17%) 305 0.639
(1.00)
0.982
(1.00)
0.0806
(0.949)
0.924
(1.00)
0.571
(0.99)
0.459
(0.966)
0.549
(0.99)
0.716
(1.00)
0.142
(0.959)
0.924
(1.00)
0.886
(1.00)
0.297
(0.959)
0.339
(0.962)
0.339
(0.962)
del 4p16 3 91 (25%) 276 0.115
(0.949)
0.337
(0.962)
0.577
(0.99)
0.131
(0.959)
0.559
(0.99)
0.479
(0.968)
0.307
(0.959)
0.757
(1.00)
0.718
(1.00)
0.746
(1.00)
0.804
(1.00)
0.718
(1.00)
0.702
(1.00)
1
(1.00)
del 4q34 3 110 (30%) 257 0.983
(1.00)
0.679
(1.00)
0.913
(1.00)
0.329
(0.962)
0.85
(1.00)
0.349
(0.962)
1
(1.00)
0.881
(1.00)
0.313
(0.959)
0.315
(0.959)
0.197
(0.959)
0.737
(1.00)
0.745
(1.00)
0.679
(1.00)
del 5p15 31 79 (22%) 288 0.355
(0.962)
0.29
(0.959)
0.902
(1.00)
0.28
(0.959)
0.199
(0.959)
0.379
(0.962)
0.273
(0.959)
0.0128
(0.69)
0.132
(0.959)
0.245
(0.959)
0.19
(0.959)
1
(1.00)
0.0211
(0.792)
0.353
(0.962)
del 5q12 1 97 (26%) 270 0.806
(1.00)
0.696
(1.00)
0.246
(0.959)
0.766
(1.00)
0.899
(1.00)
0.596
(0.999)
0.461
(0.966)
0.436
(0.966)
0.288
(0.959)
0.957
(1.00)
1
(1.00)
0.114
(0.949)
1
(1.00)
0.197
(0.959)
del 5q31 3 131 (36%) 236 0.866
(1.00)
0.914
(1.00)
0.751
(1.00)
0.613
(1.00)
0.289
(0.959)
0.49
(0.968)
0.82
(1.00)
0.888
(1.00)
0.0333
(0.935)
0.528
(0.978)
0.736
(1.00)
0.104
(0.949)
1
(1.00)
0.0545
(0.935)
del 6q21 214 (58%) 153 0.202
(0.959)
0.911
(1.00)
0.372
(0.962)
0.789
(1.00)
0.567
(0.99)
0.754
(1.00)
0.188
(0.959)
0.0267
(0.842)
0.433
(0.966)
0.234
(0.959)
0.447
(0.966)
0.526
(0.978)
1
(1.00)
0.46
(0.966)
del 6q26 221 (60%) 146 0.374
(0.962)
0.937
(1.00)
0.407
(0.966)
0.518
(0.978)
0.214
(0.959)
0.898
(1.00)
0.176
(0.959)
0.094
(0.949)
0.428
(0.966)
0.924
(1.00)
0.152
(0.959)
0.75
(1.00)
0.116
(0.949)
1
(1.00)
del 8p23 3 89 (24%) 278 0.72
(1.00)
0.383
(0.962)
0.754
(1.00)
0.859
(1.00)
0.159
(0.959)
0.0604
(0.935)
0.798
(1.00)
0.874
(1.00)
0.856
(1.00)
0.583
(0.99)
0.615
(1.00)
0.717
(1.00)
1
(1.00)
1
(1.00)
del 9p23 249 (68%) 118 0.639
(1.00)
0.412
(0.966)
0.364
(0.962)
0.75
(1.00)
0.807
(1.00)
0.821
(1.00)
0.645
(1.00)
0.664
(1.00)
0.403
(0.966)
0.536
(0.978)
0.249
(0.959)
0.131
(0.959)
0.775
(1.00)
0.0381
(0.935)
del 9p21 3 278 (76%) 89 0.948
(1.00)
0.778
(1.00)
0.207
(0.959)
0.637
(1.00)
0.77
(1.00)
0.713
(1.00)
0.307
(0.959)
0.876
(1.00)
0.717
(1.00)
0.455
(0.966)
0.0438
(0.935)
0.0179
(0.792)
1
(1.00)
0.0642
(0.938)
del 10p15 3 199 (54%) 168 0.866
(1.00)
0.781
(1.00)
0.0588
(0.935)
0.75
(1.00)
0.02
(0.792)
0.583
(0.99)
0.268
(0.959)
0.494
(0.97)
0.439
(0.966)
0.399
(0.966)
0.195
(0.959)
0.877
(1.00)
0.12
(0.949)
1
(1.00)
del 10q21 1 217 (59%) 150 0.794
(1.00)
0.427
(0.966)
0.00651
(0.547)
0.777
(1.00)
0.0494
(0.935)
0.261
(0.959)
0.662
(1.00)
0.677
(1.00)
0.634
(1.00)
0.904
(1.00)
0.0793
(0.949)
0.344
(0.962)
0.0756
(0.949)
1
(1.00)
del 10q23 31 230 (63%) 137 0.406
(0.966)
0.287
(0.959)
0.0224
(0.792)
0.633
(1.00)
0.0509
(0.935)
0.184
(0.959)
0.0682
(0.938)
0.487
(0.968)
1
(1.00)
0.677
(1.00)
0.0595
(0.935)
0.747
(1.00)
0.239
(0.959)
1
(1.00)
del 11q23 3 204 (56%) 163 0.36
(0.962)
0.48
(0.968)
0.338
(0.962)
0.65
(1.00)
0.726
(1.00)
0.745
(1.00)
0.386
(0.962)
0.891
(1.00)
0.532
(0.978)
0.588
(0.995)
0.129
(0.959)
1
(1.00)
1
(1.00)
0.705
(1.00)
del 12q23 3 92 (25%) 275 0.933
(1.00)
0.295
(0.959)
0.862
(1.00)
0.963
(1.00)
0.561
(0.99)
0.549
(0.99)
0.801
(1.00)
0.876
(1.00)
0.858
(1.00)
0.282
(0.959)
0.456
(0.966)
0.719
(1.00)
0.5
(0.978)
0.199
(0.959)
del 13q34 85 (23%) 282 0.326
(0.962)
0.402
(0.966)
0.604
(1.00)
0.872
(1.00)
0.314
(0.959)
0.835
(1.00)
0.187
(0.959)
0.12
(0.949)
0.356
(0.962)
0.348
(0.962)
0.898
(1.00)
1
(1.00)
0.686
(1.00)
0.668
(1.00)
del 14q23 3 120 (33%) 247 0.322
(0.962)
0.373
(0.962)
0.493
(0.97)
0.197
(0.959)
0.768
(1.00)
0.324
(0.962)
0.163
(0.959)
0.469
(0.968)
1
(1.00)
0.583
(0.99)
0.301
(0.959)
0.507
(0.978)
0.773
(1.00)
1
(1.00)
del 14q32 31 117 (32%) 250 0.557
(0.99)
0.314
(0.959)
0.536
(0.978)
0.386
(0.962)
0.413
(0.966)
0.135
(0.959)
0.479
(0.968)
0.469
(0.968)
0.739
(1.00)
0.646
(1.00)
0.818
(1.00)
1
(1.00)
0.765
(1.00)
1
(1.00)
del 15q13 3 84 (23%) 283 0.243
(0.959)
0.0569
(0.935)
0.56
(0.99)
0.531
(0.978)
0.0458
(0.935)
0.744
(1.00)
0.604
(1.00)
0.872
(1.00)
0.854
(1.00)
0.973
(1.00)
0.525
(0.978)
0.356
(0.962)
0.48
(0.968)
0.36
(0.962)
del 15q21 1 91 (25%) 276 0.227
(0.959)
0.0975
(0.949)
0.415
(0.966)
0.257
(0.959)
0.164
(0.959)
0.511
(0.978)
0.799
(1.00)
1
(1.00)
0.718
(1.00)
0.991
(1.00)
0.533
(0.978)
0.209
(0.959)
0.222
(0.959)
1
(1.00)
del 16p13 3 62 (17%) 305 0.215
(0.959)
0.735
(1.00)
0.248
(0.959)
0.609
(1.00)
0.223
(0.959)
0.875
(1.00)
0.558
(0.99)
0.865
(1.00)
0.0113
(0.69)
0.483
(0.968)
0.315
(0.959)
1
(1.00)
0.2
(0.959)
0.102
(0.949)
del 16q12 1 117 (32%) 250 0.425
(0.966)
0.753
(1.00)
0.295
(0.959)
0.551
(0.99)
0.543
(0.986)
0.659
(1.00)
0.634
(1.00)
0.67
(1.00)
0.616
(1.00)
0.228
(0.959)
0.49
(0.968)
0.74
(1.00)
0.545
(0.988)
0.685
(1.00)
del 16q23 1 120 (33%) 247 0.94
(1.00)
0.829
(1.00)
0.271
(0.959)
0.161
(0.959)
0.334
(0.962)
0.377
(0.962)
0.349
(0.962)
0.775
(1.00)
0.74
(1.00)
0.205
(0.959)
0.301
(0.959)
1
(1.00)
0.55
(0.99)
0.688
(1.00)
del 16q24 3 133 (36%) 234 0.983
(1.00)
0.926
(1.00)
0.136
(0.959)
0.108
(0.949)
0.264
(0.959)
0.4
(0.966)
1
(1.00)
0.89
(1.00)
0.417
(0.966)
0.228
(0.959)
0.824
(1.00)
1
(1.00)
0.339
(0.962)
0.709
(1.00)
del 17p13 3 134 (37%) 233 0.438
(0.966)
0.637
(1.00)
0.0779
(0.949)
0.458
(0.966)
0.862
(1.00)
0.987
(1.00)
0.369
(0.962)
0.677
(1.00)
0.334
(0.962)
0.887
(1.00)
0.0438
(0.935)
0.197
(0.959)
0.343
(0.962)
0.43
(0.966)
del 19p13 3 104 (28%) 263 0.464
(0.968)
0.22
(0.959)
0.72
(1.00)
0.563
(0.99)
0.815
(1.00)
0.685
(1.00)
0.631
(1.00)
1
(1.00)
0.3
(0.959)
0.921
(1.00)
0.282
(0.959)
0.604
(1.00)
1
(1.00)
0.678
(1.00)
del xp21 1 86 (23%) 281 0.105
(0.949)
0.83
(1.00)
0.777
(1.00)
0.054
(0.935)
0.411
(0.966)
0.42
(0.966)
0.123
(0.956)
0.252
(0.959)
0.356
(0.962)
0.0563
(0.935)
0.254
(0.959)
0.145
(0.959)
0.69
(1.00)
0.668
(1.00)
'amp_3p13' versus 'Time from Specimen Diagnosis to Death'

P value = 0.00025 (logrank test), Q value = 0.095

Table S1.  Gene #4: 'amp_3p13' versus Clinical Feature #1: 'Time from Specimen Diagnosis to Death'

nPatients nDeath Duration Range (Median), Month
ALL 252 124 0.0 - 346.5 (46.5)
AMP PEAK 4(3P13) MUTATED 71 26 0.8 - 346.5 (64.8)
AMP PEAK 4(3P13) WILD-TYPE 181 98 0.0 - 312.1 (36.3)

Figure S1.  Get High-res Image Gene #4: 'amp_3p13' versus Clinical Feature #1: 'Time from Specimen Diagnosis to Death'

'amp_6q12' versus 'PATHOLOGIC_STAGE'

P value = 0.00116 (Fisher's exact test), Q value = 0.22

Table S2.  Gene #9: 'amp_6q12' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

nPatients I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
ALL 13 7 29 18 28 26 14 19 15 39 15 35 54 21
AMP PEAK 9(6Q12) MUTATED 1 3 6 4 12 7 3 3 6 7 6 9 4 0
AMP PEAK 9(6Q12) WILD-TYPE 12 4 23 14 16 19 11 16 9 32 9 26 50 21

Figure S2.  Get High-res Image Gene #9: 'amp_6q12' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.00018 (Wilcoxon-test), Q value = 0.095

Table S3.  Gene #39: 'del_10q26.3' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 359 56.3 (15.7)
DEL PEAK 19(10Q26.3) MUTATED 228 54.0 (16.2)
DEL PEAK 19(10Q26.3) WILD-TYPE 131 60.4 (14.0)

Figure S3.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'GENDER'

P value = 0.000691 (Fisher's exact test), Q value = 0.17

Table S4.  Gene #40: 'del_11p15.5' versus Clinical Feature #11: 'GENDER'

nPatients FEMALE MALE
ALL 138 229
DEL PEAK 20(11P15.5) MUTATED 58 56
DEL PEAK 20(11P15.5) WILD-TYPE 80 173

Figure S4.  Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #11: 'GENDER'

Methods & Data
Input
  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/22533834/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/22507034/SKCM-TM.merged_data.txt

  • Number of patients = 367

  • Number of significantly focal cnvs = 54

  • Number of selected clinical features = 14

  • 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

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[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)