Correlation between copy number variation genes (focal events) and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1ZS2VCQ
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1ZS2VCQ
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 71 focal events and 8 clinical features across 571 patients, 11 significant findings detected with Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'AGE'.

  • amp_10p15.3 cnv correlated to 'AGE'.

  • amp_12p13.33 cnv correlated to 'AGE'.

  • amp_12p12.1 cnv correlated to 'AGE'.

  • amp_12q15 cnv correlated to 'AGE'.

  • amp_19q12 cnv correlated to 'AGE'.

  • amp_19q13.2 cnv correlated to 'AGE'.

  • amp_20q11.21 cnv correlated to 'AGE'.

  • amp_20q13.33 cnv correlated to 'AGE'.

  • del_6q27 cnv correlated to 'AGE'.

  • del_16q23.1 cnv correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		KARNOFSKY
PERFORMANCE
SCORE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 1q21 3 363 (64%) 208 0.227
(1.00) 		7.11e-06
(0.004) 		0.126
(1.00) 		0.437
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.975
(1.00) 		1
(1.00)
amp 10p15 3 250 (44%) 321 0.155
(1.00) 		0.000424
(0.236) 		0.159
(1.00) 		0.886
(1.00) 		0.584
(1.00) 		0.682
(1.00) 		0.21
(1.00) 		0.198
(1.00)
amp 12p13 33 327 (57%) 244 0.77
(1.00) 		1.89e-07
(0.000107) 		0.76
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.243
(1.00) 		1
(1.00) 		1
(1.00)
amp 12p12 1 311 (54%) 260 0.0751
(1.00) 		1.66e-08
(9.44e-06) 		0.254
(1.00) 		0.609
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.522
(1.00) 		1
(1.00)
amp 12q15 220 (39%) 351 0.201
(1.00) 		4.47e-07
(0.000252) 		0.0202
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.926
(1.00) 		0.738
(1.00)
amp 19q12 317 (56%) 254 0.442
(1.00) 		1.61e-05
(0.00905) 		0.162
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.499
(1.00) 		1
(1.00)
amp 19q13 2 241 (42%) 330 0.0202
(1.00) 		2.98e-06
(0.00168) 		0.152
(1.00) 		0.96
(1.00) 		0.576
(1.00) 		0.667
(1.00) 		0.00936
(1.00) 		0.748
(1.00)
amp 20q11 21 342 (60%) 229 0.1
(1.00) 		2.44e-08
(1.38e-05) 		1
(1.00) 		0.452
(1.00) 		1
(1.00) 		0.651
(1.00) 		0.34
(1.00) 		0.748
(1.00)
amp 20q13 33 397 (70%) 174 0.455
(1.00) 		7.42e-06
(0.00417) 		1
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.0788
(1.00) 		0.0786
(1.00) 		0.731
(1.00)
del 6q27 373 (65%) 198 0.14
(1.00) 		9.39e-05
(0.0526) 		1
(1.00) 		0.949
(1.00) 		1
(1.00) 		0.808
(1.00) 		0.907
(1.00) 		1
(1.00)
del 16q23 1 446 (78%) 125 0.219
(1.00) 		0.000392
(0.219) 		0.633
(1.00) 		0.0493
(1.00) 		1
(1.00) 		0.0385
(1.00) 		1
(1.00) 		0.247
(1.00)
amp 1p34 3 289 (51%) 282 0.0156
(1.00) 		0.0176
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.249
(1.00) 		0.532
(1.00) 		0.059
(1.00) 		1
(1.00)
amp 1q42 2 315 (55%) 256 0.177
(1.00) 		0.000866
(0.482) 		0.255
(1.00) 		0.885
(1.00) 		0.59
(1.00) 		0.885
(1.00) 		0.856
(1.00) 		0.531
(1.00)
amp 2p23 2 246 (43%) 325 0.706
(1.00) 		0.091
(1.00) 		0.76
(1.00) 		0.969
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.871
(1.00) 		1
(1.00)
amp 2q31 2 259 (45%) 312 0.155
(1.00) 		0.0227
(1.00) 		0.754
(1.00) 		0.978
(1.00) 		0.0927
(1.00) 		0.955
(1.00) 		0.771
(1.00) 		0.339
(1.00)
amp 3q26 2 477 (84%) 94 0.863
(1.00) 		0.00217
(1.00) 		1
(1.00) 		0.0185
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.536
(1.00) 		0.649
(1.00)
amp 4p16 3 158 (28%) 413 0.541
(1.00) 		0.65
(1.00) 		0.726
(1.00) 		0.368
(1.00) 		0.187
(1.00) 		0.643
(1.00) 		0.535
(1.00) 		0.729
(1.00)
amp 4q13 3 113 (20%) 458 0.177
(1.00) 		0.191
(1.00) 		0.592
(1.00) 		0.479
(1.00) 		0.485
(1.00) 		0.128
(1.00) 		0.502
(1.00) 		1
(1.00)
amp 5p15 33 305 (53%) 266 0.0807
(1.00) 		0.0109
(1.00) 		0.753
(1.00) 		0.873
(1.00) 		0.6
(1.00) 		0.105
(1.00) 		0.885
(1.00) 		0.753
(1.00)
amp 6p22 3 298 (52%) 273 0.0953
(1.00) 		0.00297
(1.00) 		1
(1.00) 		0.371
(1.00) 		1
(1.00) 		0.903
(1.00) 		0.589
(1.00) 		0.344
(1.00)
amp 7q36 3 314 (55%) 257 0.146
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.105
(1.00) 		0.591
(1.00) 		0.956
(1.00) 		0.0771
(1.00) 		0.344
(1.00)
amp 8p11 21 209 (37%) 362 0.226
(1.00) 		0.000548
(0.305) 		0.123
(1.00) 		0.827
(1.00) 		0.558
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00)
amp 8q24 21 453 (79%) 118 0.484
(1.00) 		0.0953
(1.00) 		1
(1.00) 		0.721
(1.00) 		0.501
(1.00) 		0.921
(1.00) 		0.709
(1.00) 		0.43
(1.00)
amp 10q22 3 181 (32%) 390 0.36
(1.00) 		0.116
(1.00) 		0.1
(1.00) 		0.96
(1.00) 		1
(1.00) 		0.399
(1.00) 		0.339
(1.00) 		1
(1.00)
amp 11q14 1 253 (44%) 318 0.583
(1.00) 		0.553
(1.00) 		0.255
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.883
(1.00) 		0.525
(1.00)
amp 14q11 2 146 (26%) 425 0.787
(1.00) 		0.0442
(1.00) 		0.129
(1.00) 		0.386
(1.00) 		0.162
(1.00) 		0.625
(1.00) 		0.433
(1.00) 		0.138
(1.00)
amp 14q32 33 155 (27%) 416 0.483
(1.00) 		0.0173
(1.00) 		0.718
(1.00) 		0.895
(1.00) 		0.0197
(1.00) 		1
(1.00) 		0.73
(1.00) 		0.716
(1.00)
amp 15q26 3 159 (28%) 412 0.086
(1.00) 		0.192
(1.00) 		0.733
(1.00) 		0.731
(1.00) 		0.564
(1.00) 		0.797
(1.00) 		0.516
(1.00) 		0.732
(1.00)
amp 17q25 3 212 (37%) 359 0.15
(1.00) 		0.75
(1.00) 		0.26
(1.00) 		0.957
(1.00) 		1
(1.00) 		0.0737
(1.00) 		0.706
(1.00) 		1
(1.00)
amp 18q11 2 139 (24%) 432 0.755
(1.00) 		0.106
(1.00) 		0.116
(1.00) 		0.363
(1.00) 		0.568
(1.00) 		0.891
(1.00) 		0.573
(1.00) 		0.263
(1.00)
amp 19p13 12 312 (55%) 259 0.261
(1.00) 		0.0441
(1.00) 		0.456
(1.00) 		0.227
(1.00) 		0.593
(1.00) 		0.312
(1.00) 		0.956
(1.00) 		1
(1.00)
amp 20p13 314 (55%) 257 0.305
(1.00) 		0.00503
(1.00) 		0.752
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.161
(1.00) 		0.523
(1.00)
amp 22q12 2 91 (16%) 480 0.519
(1.00) 		0.0397
(1.00) 		0.509
(1.00) 		0.25
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.977
(1.00) 		0.168
(1.00)
amp xp11 23 158 (28%) 413 0.143
(1.00) 		0.104
(1.00) 		0.0674
(1.00) 		0.739
(1.00) 		0.564
(1.00) 		0.285
(1.00) 		0.932
(1.00) 		1
(1.00)
amp xq28 216 (38%) 355 0.507
(1.00) 		0.627
(1.00) 		0.776
(1.00) 		0.337
(1.00) 		0.0537
(1.00) 		0.552
(1.00) 		0.827
(1.00) 		0.328
(1.00)
del 1p36 11 265 (46%) 306 0.175
(1.00) 		0.282
(1.00) 		0.751
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.378
(1.00) 		0.523
(1.00)
del 1q41 94 (16%) 477 0.899
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.952
(1.00) 		0.418
(1.00) 		0.738
(1.00) 		0.0614
(1.00) 		0.375
(1.00)
del 2p25 3 120 (21%) 451 0.911
(1.00) 		0.458
(1.00) 		0.618
(1.00) 		0.938
(1.00) 		0.508
(1.00) 		0.0255
(1.00) 		0.166
(1.00) 		0.453
(1.00)
del 2q22 1 134 (23%) 437 0.351
(1.00) 		0.288
(1.00) 		0.663
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.433
(1.00) 		0.0628
(1.00)
del 2q37 3 172 (30%) 399 0.423
(1.00) 		0.0204
(1.00) 		0.354
(1.00) 		0.126
(1.00) 		0.217
(1.00) 		0.645
(1.00) 		0.721
(1.00) 		1
(1.00)
del 3p26 2 206 (36%) 365 0.749
(1.00) 		0.00396
(1.00) 		0.125
(1.00) 		0.328
(1.00) 		0.0465
(1.00) 		0.476
(1.00) 		0.467
(1.00) 		1
(1.00)
del 3q13 31 84 (15%) 487 0.442
(1.00) 		0.801
(1.00) 		1
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.854
(1.00) 		1
(1.00)
del 4q22 1 389 (68%) 182 0.553
(1.00) 		0.861
(1.00) 		0.792
(1.00) 		0.629
(1.00) 		1
(1.00) 		0.852
(1.00) 		0.828
(1.00) 		0.173
(1.00)
del 4q34 3 415 (73%) 156 0.969
(1.00) 		0.475
(1.00) 		0.723
(1.00) 		0.184
(1.00) 		0.566
(1.00) 		0.484
(1.00) 		0.908
(1.00) 		0.0674
(1.00)
del 5q12 1 349 (61%) 222 0.918
(1.00) 		0.682
(1.00) 		0.771
(1.00) 		0.149
(1.00) 		0.563
(1.00) 		0.369
(1.00) 		0.133
(1.00) 		1
(1.00)
del 5q13 2 413 (72%) 158 0.238
(1.00) 		0.999
(1.00) 		0.728
(1.00) 		0.0767
(1.00) 		0.187
(1.00) 		0.171
(1.00) 		0.284
(1.00) 		1
(1.00)
del 7p22 1 250 (44%) 321 0.07
(1.00) 		0.0089
(1.00) 		0.755
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.665
(1.00) 		0.75
(1.00)
del 8p23 3 383 (67%) 188 0.202
(1.00) 		0.0649
(1.00) 		1
(1.00) 		0.637
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.901
(1.00) 		0.175
(1.00)
del 8p21 2 400 (70%) 171 0.61
(1.00) 		0.0731
(1.00) 		1
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.293
(1.00)
del 9p24 3 259 (45%) 312 0.627
(1.00) 		0.0142
(1.00) 		0.453
(1.00) 		0.648
(1.00) 		0.593
(1.00) 		0.73
(1.00) 		0.906
(1.00) 		1
(1.00)
del 9q34 13 340 (60%) 231 0.993
(1.00) 		0.0592
(1.00) 		0.765
(1.00) 		0.837
(1.00) 		0.276
(1.00) 		0.757
(1.00) 		0.477
(1.00) 		1
(1.00)
del 10p15 3 117 (20%) 454 0.363
(1.00) 		0.894
(1.00) 		0.601
(1.00) 		0.765
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.274
(1.00) 		0.696
(1.00)
del 10q24 2 250 (44%) 321 0.243
(1.00) 		0.0547
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.584
(1.00) 		1
(1.00) 		0.104
(1.00) 		1
(1.00)
del 11p15 5 340 (60%) 231 0.128
(1.00) 		0.383
(1.00) 		0.0263
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.665
(1.00) 		0.602
(1.00) 		1
(1.00)
del 11q25 200 (35%) 371 0.746
(1.00) 		0.0389
(1.00) 		0.232
(1.00) 		0.396
(1.00) 		0.282
(1.00) 		0.703
(1.00) 		0.948
(1.00) 		0.0379
(1.00)
del 12q24 33 214 (37%) 357 0.852
(1.00) 		0.0796
(1.00) 		0.13
(1.00) 		0.778
(1.00) 		0.296
(1.00) 		0.0673
(1.00) 		0.635
(1.00) 		0.0366
(1.00)
del 13q14 2 358 (63%) 213 0.0762
(1.00) 		0.401
(1.00) 		0.78
(1.00) 		0.969
(1.00) 		0.559
(1.00) 		0.226
(1.00) 		0.123
(1.00) 		0.746
(1.00)
del 14q23 3 301 (53%) 270 0.969
(1.00) 		0.515
(1.00) 		0.47
(1.00) 		0.126
(1.00) 		0.105
(1.00) 		0.369
(1.00) 		0.255
(1.00) 		0.114
(1.00)
del 15q11 2 295 (52%) 276 0.855
(1.00) 		0.00382
(1.00) 		0.25
(1.00) 		0.682
(1.00) 		0.25
(1.00) 		0.71
(1.00) 		0.29
(1.00) 		0.752
(1.00)
del 15q15 1 359 (63%) 212 0.835
(1.00) 		0.00492
(1.00) 		0.41
(1.00) 		0.534
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.327
(1.00)
del 16p13 3 308 (54%) 263 0.965
(1.00) 		0.699
(1.00) 		0.753
(1.00) 		0.399
(1.00) 		0.597
(1.00) 		0.966
(1.00) 		0.931
(1.00) 		0.521
(1.00)
del 16q22 1 456 (80%) 115 0.725
(1.00) 		0.0129
(1.00) 		0.187
(1.00) 		0.111
(1.00) 		1
(1.00) 		0.0393
(1.00) 		0.952
(1.00) 		0.425
(1.00)
del 17p12 485 (85%) 86 0.979
(1.00) 		0.784
(1.00) 		0.481
(1.00) 		0.816
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.858
(1.00) 		0.653
(1.00)
del 17q11 2 466 (82%) 105 0.762
(1.00) 		0.0126
(1.00) 		0.0665
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.956
(1.00) 		0.624
(1.00) 		1
(1.00)
del 18q23 376 (66%) 195 0.696
(1.00) 		0.617
(1.00) 		0.222
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.0808
(1.00) 		0.246
(1.00) 		1
(1.00)
del 19p13 3 504 (88%) 67 0.23
(1.00) 		0.027
(1.00) 		1
(1.00) 		0.0822
(1.00) 		1
(1.00) 		1
(1.00) 		0.0751
(1.00) 		1
(1.00)
del 19q13 33 294 (51%) 277 0.445
(1.00) 		0.568
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.249
(1.00) 		0.384
(1.00) 		0.16
(1.00) 		0.112
(1.00)
del 19q13 43 280 (49%) 291 0.457
(1.00) 		0.0361
(1.00) 		1
(1.00) 		0.0607
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.153
(1.00) 		0.207
(1.00)
del 21q22 3 223 (39%) 348 0.436
(1.00) 		0.434
(1.00) 		0.773
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.691
(1.00) 		0.329
(1.00)
del 22q13 32 496 (87%) 75 0.8
(1.00) 		0.856
(1.00) 		0.438
(1.00) 		0.387
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.814
(1.00) 		1
(1.00)
del xp21 1 352 (62%) 219 0.978
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.754
(1.00) 		0.289
(1.00) 		0.785
(1.00) 		0.922
(1.00) 		0.746
(1.00)
'amp_1q21.3' versus 'AGE'

P value = 7.11e-06 (Wilcoxon-test), Q value = 0.004

Table S1.  Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 2(1Q21.3) MUTATED 350 61.5 (10.9)
AMP PEAK 2(1Q21.3) WILD-TYPE 200 56.8 (12.1)

Figure S1.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'AGE'

'amp_10p15.3' versus 'AGE'

P value = 0.000424 (Wilcoxon-test), Q value = 0.24

Table S2.  Gene #14: 'amp_10p15.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 14(10P15.3) MUTATED 244 61.7 (11.2)
AMP PEAK 14(10P15.3) WILD-TYPE 306 58.3 (11.7)

Figure S2.  Get High-res Image Gene #14: 'amp_10p15.3' versus Clinical Feature #2: 'AGE'

'amp_12p13.33' versus 'AGE'

P value = 1.89e-07 (Wilcoxon-test), Q value = 0.00011

Table S3.  Gene #17: 'amp_12p13.33' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 17(12P13.33) MUTATED 315 62.1 (10.8)
AMP PEAK 17(12P13.33) WILD-TYPE 235 56.8 (11.9)

Figure S3.  Get High-res Image Gene #17: 'amp_12p13.33' versus Clinical Feature #2: 'AGE'

'amp_12p12.1' versus 'AGE'

P value = 1.66e-08 (Wilcoxon-test), Q value = 9.4e-06

Table S4.  Gene #18: 'amp_12p12.1' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 18(12P12.1) MUTATED 297 62.4 (11.2)
AMP PEAK 18(12P12.1) WILD-TYPE 253 56.8 (11.3)

Figure S4.  Get High-res Image Gene #18: 'amp_12p12.1' versus Clinical Feature #2: 'AGE'

'amp_12q15' versus 'AGE'

P value = 4.47e-07 (Wilcoxon-test), Q value = 0.00025

Table S5.  Gene #19: 'amp_12q15' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 19(12Q15) MUTATED 206 63.0 (11.3)
AMP PEAK 19(12Q15) WILD-TYPE 344 57.9 (11.4)

Figure S5.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #2: 'AGE'

'amp_19q12' versus 'AGE'

P value = 1.61e-05 (Wilcoxon-test), Q value = 0.009

Table S6.  Gene #26: 'amp_19q12' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 26(19Q12) MUTATED 306 61.8 (11.1)
AMP PEAK 26(19Q12) WILD-TYPE 244 57.4 (11.8)

Figure S6.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #2: 'AGE'

'amp_19q13.2' versus 'AGE'

P value = 2.98e-06 (Wilcoxon-test), Q value = 0.0017

Table S7.  Gene #27: 'amp_19q13.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 27(19Q13.2) MUTATED 234 62.5 (11.2)
AMP PEAK 27(19Q13.2) WILD-TYPE 316 57.8 (11.5)

Figure S7.  Get High-res Image Gene #27: 'amp_19q13.2' versus Clinical Feature #2: 'AGE'

'amp_20q11.21' versus 'AGE'

P value = 2.44e-08 (Wilcoxon-test), Q value = 1.4e-05

Table S8.  Gene #29: 'amp_20q11.21' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 29(20Q11.21) MUTATED 329 62.1 (11.5)
AMP PEAK 29(20Q11.21) WILD-TYPE 221 56.4 (10.9)

Figure S8.  Get High-res Image Gene #29: 'amp_20q11.21' versus Clinical Feature #2: 'AGE'

'amp_20q13.33' versus 'AGE'

P value = 7.42e-06 (Wilcoxon-test), Q value = 0.0042

Table S9.  Gene #30: 'amp_20q13.33' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
AMP PEAK 30(20Q13.33) MUTATED 384 61.3 (11.5)
AMP PEAK 30(20Q13.33) WILD-TYPE 166 56.5 (11.1)

Figure S9.  Get High-res Image Gene #30: 'amp_20q13.33' versus Clinical Feature #2: 'AGE'

'del_6q27' versus 'AGE'

P value = 9.39e-05 (Wilcoxon-test), Q value = 0.053

Table S10.  Gene #45: 'del_6q27' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
DEL PEAK 12(6Q27) MUTATED 358 58.4 (11.4)
DEL PEAK 12(6Q27) WILD-TYPE 192 62.4 (11.5)

Figure S10.  Get High-res Image Gene #45: 'del_6q27' versus Clinical Feature #2: 'AGE'

'del_16q23.1' versus 'AGE'

P value = 0.000392 (Wilcoxon-test), Q value = 0.22

Table S11.  Gene #62: 'del_16q23.1' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
DEL PEAK 29(16Q23.1) MUTATED 432 60.8 (11.5)
DEL PEAK 29(16Q23.1) WILD-TYPE 118 56.3 (11.3)

Figure S11.  Get High-res Image Gene #62: 'del_16q23.1' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

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

  • Clinical data file = OV-TP.merged_data.txt

  • Number of patients = 571

  • Number of significantly focal cnvs = 71

  • Number of selected clinical features = 8

  • 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)
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