Correlation between copy number variation genes (focal events) and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
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 (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1N58K50
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 68 focal events and 8 clinical features across 562 patients, 11 significant findings detected with Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'AGE'.

  • amp_1q42.2 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_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 68 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 3 358 (64%) 204 0.246
(1.00)
4.41e-06
(0.00239)
0.126
(1.00)
0.473
(1.00)
1
(1.00)
0.349
(1.00)
0.982
(1.00)
1
(1.00)
amp 1q42 2 308 (55%) 254 0.196
(1.00)
0.000447
(0.239)
0.251
(1.00)
0.795
(1.00)
0.592
(1.00)
0.876
(1.00)
0.675
(1.00)
0.533
(1.00)
amp 10p15 3 244 (43%) 318 0.166
(1.00)
0.00045
(0.241)
0.156
(1.00)
0.947
(1.00)
0.582
(1.00)
0.759
(1.00)
0.0231
(1.00)
0.196
(1.00)
amp 12p13 33 320 (57%) 242 0.63
(1.00)
3.44e-07
(0.000186)
0.758
(1.00)
0.534
(1.00)
1
(1.00)
0.343
(1.00)
0.947
(1.00)
1
(1.00)
amp 12p12 1 305 (54%) 257 0.0495
(1.00)
3.9e-08
(2.12e-05)
0.25
(1.00)
0.286
(1.00)
0.595
(1.00)
1
(1.00)
0.443
(1.00)
1
(1.00)
amp 19q12 315 (56%) 247 0.479
(1.00)
1.57e-05
(0.00843)
0.158
(1.00)
0.616
(1.00)
1
(1.00)
1
(1.00)
0.466
(1.00)
1
(1.00)
amp 19q13 2 238 (42%) 324 0.0118
(1.00)
7.93e-06
(0.00428)
0.153
(1.00)
0.96
(1.00)
0.577
(1.00)
0.212
(1.00)
0.00574
(1.00)
0.748
(1.00)
amp 20q11 21 335 (60%) 227 0.0825
(1.00)
4.53e-08
(2.46e-05)
1
(1.00)
0.375
(1.00)
1
(1.00)
0.582
(1.00)
0.34
(1.00)
0.749
(1.00)
amp 20q13 33 389 (69%) 173 0.392
(1.00)
1.05e-05
(0.00564)
1
(1.00)
0.808
(1.00)
1
(1.00)
0.0805
(1.00)
0.101
(1.00)
0.73
(1.00)
del 6q27 375 (67%) 187 0.339
(1.00)
0.000444
(0.238)
1
(1.00)
0.618
(1.00)
1
(1.00)
0.871
(1.00)
0.954
(1.00)
1
(1.00)
del 16q23 1 439 (78%) 123 0.238
(1.00)
0.000273
(0.146)
0.631
(1.00)
0.116
(1.00)
1
(1.00)
0.0948
(1.00)
1
(1.00)
0.244
(1.00)
amp 1p34 3 285 (51%) 277 0.0217
(1.00)
0.0153
(1.00)
1
(1.00)
0.833
(1.00)
0.249
(1.00)
0.476
(1.00)
0.0775
(1.00)
1
(1.00)
amp 2p23 2 240 (43%) 322 0.735
(1.00)
0.107
(1.00)
0.757
(1.00)
0.901
(1.00)
1
(1.00)
0.662
(1.00)
0.93
(1.00)
1
(1.00)
amp 2q31 2 256 (46%) 306 0.145
(1.00)
0.0179
(1.00)
0.754
(1.00)
0.621
(1.00)
0.0939
(1.00)
0.873
(1.00)
0.831
(1.00)
0.338
(1.00)
amp 3q26 2 469 (83%) 93 0.879
(1.00)
0.00147
(0.782)
1
(1.00)
0.0138
(1.00)
1
(1.00)
0.778
(1.00)
0.443
(1.00)
0.648
(1.00)
amp 4p16 3 156 (28%) 406 0.587
(1.00)
0.673
(1.00)
0.725
(1.00)
0.156
(1.00)
0.188
(1.00)
0.53
(1.00)
0.213
(1.00)
0.734
(1.00)
amp 4q13 3 110 (20%) 452 0.294
(1.00)
0.209
(1.00)
0.584
(1.00)
0.219
(1.00)
0.48
(1.00)
0.412
(1.00)
0.414
(1.00)
1
(1.00)
amp 5p15 33 301 (54%) 261 0.0818
(1.00)
0.00694
(1.00)
0.749
(1.00)
0.795
(1.00)
0.6
(1.00)
0.0477
(1.00)
0.873
(1.00)
0.753
(1.00)
amp 6p22 3 293 (52%) 269 0.119
(1.00)
0.00585
(1.00)
1
(1.00)
0.523
(1.00)
1
(1.00)
0.511
(1.00)
0.591
(1.00)
0.343
(1.00)
amp 7q36 3 306 (54%) 256 0.134
(1.00)
0.621
(1.00)
1
(1.00)
0.0223
(1.00)
0.594
(1.00)
0.213
(1.00)
0.154
(1.00)
0.348
(1.00)
amp 8p11 21 206 (37%) 356 0.245
(1.00)
0.00102
(0.545)
0.124
(1.00)
0.884
(1.00)
0.558
(1.00)
0.16
(1.00)
1
(1.00)
1
(1.00)
amp 8q24 21 444 (79%) 118 0.489
(1.00)
0.0897
(1.00)
1
(1.00)
0.76
(1.00)
0.508
(1.00)
0.392
(1.00)
0.639
(1.00)
0.437
(1.00)
amp 10q22 3 178 (32%) 384 0.562
(1.00)
0.157
(1.00)
0.0975
(1.00)
0.96
(1.00)
1
(1.00)
0.455
(1.00)
0.267
(1.00)
1
(1.00)
amp 11q14 1 249 (44%) 313 0.473
(1.00)
0.503
(1.00)
0.254
(1.00)
0.365
(1.00)
1
(1.00)
1
(1.00)
0.829
(1.00)
0.524
(1.00)
amp 14q11 2 144 (26%) 418 0.738
(1.00)
0.0588
(1.00)
0.129
(1.00)
0.394
(1.00)
0.163
(1.00)
0.837
(1.00)
0.519
(1.00)
0.139
(1.00)
amp 14q32 33 152 (27%) 410 0.503
(1.00)
0.0108
(1.00)
0.717
(1.00)
0.424
(1.00)
0.0195
(1.00)
1
(1.00)
0.793
(1.00)
0.717
(1.00)
amp 15q26 3 157 (28%) 405 0.0685
(1.00)
0.182
(1.00)
0.735
(1.00)
0.443
(1.00)
0.564
(1.00)
1
(1.00)
0.521
(1.00)
0.731
(1.00)
amp 17q25 3 209 (37%) 353 0.0801
(1.00)
0.657
(1.00)
0.262
(1.00)
0.67
(1.00)
1
(1.00)
0.0894
(1.00)
0.655
(1.00)
1
(1.00)
amp 18q11 2 138 (25%) 424 0.666
(1.00)
0.0869
(1.00)
0.117
(1.00)
0.162
(1.00)
0.571
(1.00)
0.836
(1.00)
0.659
(1.00)
0.264
(1.00)
amp 19p13 12 306 (54%) 256 0.233
(1.00)
0.0513
(1.00)
0.456
(1.00)
0.576
(1.00)
0.594
(1.00)
0.416
(1.00)
0.961
(1.00)
1
(1.00)
amp 20p13 311 (55%) 251 0.281
(1.00)
0.00131
(0.698)
0.753
(1.00)
0.155
(1.00)
1
(1.00)
0.382
(1.00)
0.824
(1.00)
0.522
(1.00)
amp 22q12 2 89 (16%) 473 0.557
(1.00)
0.0375
(1.00)
0.506
(1.00)
0.497
(1.00)
1
(1.00)
1
(1.00)
0.948
(1.00)
0.167
(1.00)
amp xp11 23 154 (27%) 408 0.247
(1.00)
0.0894
(1.00)
0.0686
(1.00)
0.441
(1.00)
0.565
(1.00)
0.33
(1.00)
0.833
(1.00)
1
(1.00)
amp xq28 214 (38%) 348 0.481
(1.00)
0.652
(1.00)
0.78
(1.00)
0.598
(1.00)
0.0547
(1.00)
0.876
(1.00)
0.831
(1.00)
0.329
(1.00)
del 1p36 11 263 (47%) 299 0.183
(1.00)
0.272
(1.00)
0.75
(1.00)
0.323
(1.00)
1
(1.00)
1
(1.00)
0.518
(1.00)
0.526
(1.00)
del 1q41 92 (16%) 470 0.821
(1.00)
0.386
(1.00)
1
(1.00)
0.628
(1.00)
0.416
(1.00)
0.605
(1.00)
0.0645
(1.00)
0.373
(1.00)
del 2p25 3 120 (21%) 442 0.922
(1.00)
0.437
(1.00)
0.623
(1.00)
0.971
(1.00)
0.514
(1.00)
0.022
(1.00)
0.496
(1.00)
0.461
(1.00)
del 2q22 1 133 (24%) 429 0.412
(1.00)
0.277
(1.00)
0.664
(1.00)
0.558
(1.00)
1
(1.00)
0.644
(1.00)
0.495
(1.00)
0.0673
(1.00)
del 2q37 3 170 (30%) 392 0.472
(1.00)
0.0259
(1.00)
0.358
(1.00)
0.503
(1.00)
0.219
(1.00)
0.172
(1.00)
0.42
(1.00)
0.492
(1.00)
del 3p26 2 206 (37%) 356 0.764
(1.00)
0.00327
(1.00)
0.125
(1.00)
0.34
(1.00)
0.0488
(1.00)
0.287
(1.00)
0.841
(1.00)
1
(1.00)
del 4q22 1 384 (68%) 178 0.659
(1.00)
0.795
(1.00)
0.79
(1.00)
0.637
(1.00)
1
(1.00)
0.846
(1.00)
0.815
(1.00)
0.173
(1.00)
del 4q34 3 410 (73%) 152 0.956
(1.00)
0.489
(1.00)
0.718
(1.00)
0.301
(1.00)
0.567
(1.00)
0.571
(1.00)
0.954
(1.00)
0.0673
(1.00)
del 5q11 2 341 (61%) 221 0.767
(1.00)
0.816
(1.00)
0.771
(1.00)
0.309
(1.00)
0.565
(1.00)
0.209
(1.00)
0.087
(1.00)
1
(1.00)
del 5q13 2 406 (72%) 156 0.245
(1.00)
0.895
(1.00)
0.732
(1.00)
0.148
(1.00)
0.188
(1.00)
0.24
(1.00)
0.215
(1.00)
1
(1.00)
del 7p22 1 245 (44%) 317 0.0696
(1.00)
0.0108
(1.00)
0.758
(1.00)
0.27
(1.00)
1
(1.00)
0.18
(1.00)
0.693
(1.00)
0.749
(1.00)
del 8p23 3 378 (67%) 184 0.19
(1.00)
0.0623
(1.00)
1
(1.00)
0.91
(1.00)
1
(1.00)
0.86
(1.00)
0.905
(1.00)
0.176
(1.00)
del 8p21 2 394 (70%) 168 0.712
(1.00)
0.0634
(1.00)
1
(1.00)
0.577
(1.00)
1
(1.00)
0.438
(1.00)
1
(1.00)
0.293
(1.00)
del 9p24 3 255 (45%) 307 0.755
(1.00)
0.0111
(1.00)
0.453
(1.00)
0.95
(1.00)
0.593
(1.00)
0.75
(1.00)
0.892
(1.00)
1
(1.00)
del 9q34 13 336 (60%) 226 0.905
(1.00)
0.101
(1.00)
0.769
(1.00)
0.717
(1.00)
0.277
(1.00)
0.5
(1.00)
0.685
(1.00)
0.745
(1.00)
del 10p15 3 117 (21%) 445 0.368
(1.00)
0.92
(1.00)
0.606
(1.00)
0.792
(1.00)
0.504
(1.00)
1
(1.00)
0.305
(1.00)
0.695
(1.00)
del 10q24 2 245 (44%) 317 0.268
(1.00)
0.127
(1.00)
1
(1.00)
0.181
(1.00)
0.583
(1.00)
1
(1.00)
0.0262
(1.00)
1
(1.00)
del 11p15 5 332 (59%) 230 0.115
(1.00)
0.383
(1.00)
0.0271
(1.00)
0.299
(1.00)
1
(1.00)
0.873
(1.00)
0.852
(1.00)
1
(1.00)
del 11q25 193 (34%) 369 0.707
(1.00)
0.0672
(1.00)
0.225
(1.00)
0.31
(1.00)
0.272
(1.00)
0.252
(1.00)
0.916
(1.00)
0.036
(1.00)
del 12q24 33 211 (38%) 351 0.822
(1.00)
0.081
(1.00)
0.129
(1.00)
0.842
(1.00)
0.295
(1.00)
0.0412
(1.00)
0.59
(1.00)
0.0372
(1.00)
del 13q14 2 352 (63%) 210 0.0842
(1.00)
0.436
(1.00)
0.78
(1.00)
0.771
(1.00)
0.559
(1.00)
0.331
(1.00)
0.157
(1.00)
0.745
(1.00)
del 14q23 3 296 (53%) 266 0.817
(1.00)
0.44
(1.00)
0.473
(1.00)
0.0469
(1.00)
0.105
(1.00)
0.76
(1.00)
0.276
(1.00)
0.113
(1.00)
del 15q15 1 356 (63%) 206 0.817
(1.00)
0.0039
(1.00)
0.412
(1.00)
0.318
(1.00)
0.302
(1.00)
1
(1.00)
0.652
(1.00)
0.328
(1.00)
del 16p13 3 303 (54%) 259 0.949
(1.00)
0.769
(1.00)
0.752
(1.00)
0.399
(1.00)
0.597
(1.00)
1
(1.00)
0.806
(1.00)
0.521
(1.00)
del 16q22 1 449 (80%) 113 0.765
(1.00)
0.00983
(1.00)
0.187
(1.00)
0.273
(1.00)
1
(1.00)
0.167
(1.00)
0.963
(1.00)
0.421
(1.00)
del 17p12 477 (85%) 85 0.974
(1.00)
0.823
(1.00)
0.485
(1.00)
0.765
(1.00)
1
(1.00)
0.328
(1.00)
1
(1.00)
0.657
(1.00)
del 17q11 2 460 (82%) 102 0.542
(1.00)
0.0115
(1.00)
0.0673
(1.00)
0.759
(1.00)
1
(1.00)
0.873
(1.00)
0.481
(1.00)
1
(1.00)
del 18q23 372 (66%) 190 0.817
(1.00)
0.426
(1.00)
0.216
(1.00)
0.668
(1.00)
1
(1.00)
1
(1.00)
0.452
(1.00)
0.311
(1.00)
del 19p13 3 495 (88%) 67 0.231
(1.00)
0.0291
(1.00)
1
(1.00)
0.0707
(1.00)
1
(1.00)
0.494
(1.00)
0.186
(1.00)
1
(1.00)
del 19q13 33 291 (52%) 271 0.527
(1.00)
0.509
(1.00)
1
(1.00)
0.239
(1.00)
0.25
(1.00)
0.356
(1.00)
0.0792
(1.00)
0.113
(1.00)
del 19q13 43 275 (49%) 287 0.41
(1.00)
0.0314
(1.00)
1
(1.00)
0.267
(1.00)
1
(1.00)
0.339
(1.00)
0.143
(1.00)
0.205
(1.00)
del 21q22 3 220 (39%) 342 0.405
(1.00)
0.408
(1.00)
0.771
(1.00)
0.756
(1.00)
1
(1.00)
0.662
(1.00)
0.678
(1.00)
0.329
(1.00)
del 22q13 32 489 (87%) 73 0.996
(1.00)
0.997
(1.00)
0.433
(1.00)
0.766
(1.00)
1
(1.00)
0.673
(1.00)
0.786
(1.00)
1
(1.00)
del xp21 1 347 (62%) 215 0.971
(1.00)
0.39
(1.00)
1
(1.00)
0.99
(1.00)
0.29
(1.00)
0.761
(1.00)
0.648
(1.00)
0.536
(1.00)
'amp_1q21.3' versus 'AGE'

P value = 4.41e-06 (Wilcoxon-test), Q value = 0.0024

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 2(1Q21.3) MUTATED 345 61.6 (11.0)
AMP PEAK 2(1Q21.3) WILD-TYPE 196 56.7 (12.1)

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

'amp_1q42.2' versus 'AGE'

P value = 0.000447 (Wilcoxon-test), Q value = 0.24

Table S2.  Gene #3: 'amp_1q42.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 3(1Q42.2) MUTATED 295 61.4 (11.3)
AMP PEAK 3(1Q42.2) WILD-TYPE 246 57.9 (11.7)

Figure S2.  Get High-res Image Gene #3: 'amp_1q42.2' versus Clinical Feature #2: 'AGE'

'amp_10p15.3' versus 'AGE'

P value = 0.00045 (Wilcoxon-test), Q value = 0.24

Table S3.  Gene #14: 'amp_10p15.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 14(10P15.3) MUTATED 238 61.7 (11.2)
AMP PEAK 14(10P15.3) WILD-TYPE 303 58.3 (11.7)

Figure S3.  Get High-res Image Gene #14: 'amp_10p15.3' versus Clinical Feature #2: 'AGE'

'amp_12p13.33' versus 'AGE'

P value = 3.44e-07 (Wilcoxon-test), Q value = 0.00019

Table S4.  Gene #17: 'amp_12p13.33' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 17(12P13.33) MUTATED 308 62.0 (10.9)
AMP PEAK 17(12P13.33) WILD-TYPE 233 56.8 (11.9)

Figure S4.  Get High-res Image Gene #17: 'amp_12p13.33' versus Clinical Feature #2: 'AGE'

'amp_12p12.1' versus 'AGE'

P value = 3.9e-08 (Wilcoxon-test), Q value = 2.1e-05

Table S5.  Gene #18: 'amp_12p12.1' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 18(12P12.1) MUTATED 291 62.4 (11.2)
AMP PEAK 18(12P12.1) WILD-TYPE 250 56.8 (11.3)

Figure S5.  Get High-res Image Gene #18: 'amp_12p12.1' versus Clinical Feature #2: 'AGE'

'amp_19q12' versus 'AGE'

P value = 1.57e-05 (Wilcoxon-test), Q value = 0.0084

Table S6.  Gene #25: 'amp_19q12' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 25(19Q12) MUTATED 304 61.7 (11.1)
AMP PEAK 25(19Q12) WILD-TYPE 237 57.3 (11.8)

Figure S6.  Get High-res Image Gene #25: 'amp_19q12' versus Clinical Feature #2: 'AGE'

'amp_19q13.2' versus 'AGE'

P value = 7.93e-06 (Wilcoxon-test), Q value = 0.0043

Table S7.  Gene #26: 'amp_19q13.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 26(19Q13.2) MUTATED 231 62.4 (11.2)
AMP PEAK 26(19Q13.2) WILD-TYPE 310 57.8 (11.6)

Figure S7.  Get High-res Image Gene #26: 'amp_19q13.2' versus Clinical Feature #2: 'AGE'

'amp_20q11.21' versus 'AGE'

P value = 4.53e-08 (Wilcoxon-test), Q value = 2.5e-05

Table S8.  Gene #28: 'amp_20q11.21' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 28(20Q11.21) MUTATED 322 62.1 (11.5)
AMP PEAK 28(20Q11.21) WILD-TYPE 219 56.4 (10.9)

Figure S8.  Get High-res Image Gene #28: 'amp_20q11.21' versus Clinical Feature #2: 'AGE'

'amp_20q13.33' versus 'AGE'

P value = 1.05e-05 (Wilcoxon-test), Q value = 0.0056

Table S9.  Gene #29: 'amp_20q13.33' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 29(20Q13.33) MUTATED 376 61.2 (11.6)
AMP PEAK 29(20Q13.33) WILD-TYPE 165 56.5 (11.1)

Figure S9.  Get High-res Image Gene #29: 'amp_20q13.33' versus Clinical Feature #2: 'AGE'

'del_6q27' versus 'AGE'

P value = 0.000444 (Wilcoxon-test), Q value = 0.24

Table S10.  Gene #43: 'del_6q27' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
DEL PEAK 11(6Q27) MUTATED 360 58.6 (11.5)
DEL PEAK 11(6Q27) WILD-TYPE 181 62.2 (11.6)

Figure S10.  Get High-res Image Gene #43: 'del_6q27' versus Clinical Feature #2: 'AGE'

'del_16q23.1' versus 'AGE'

P value = 0.000273 (Wilcoxon-test), Q value = 0.15

Table S11.  Gene #59: 'del_16q23.1' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
DEL PEAK 27(16Q23.1) MUTATED 425 60.8 (11.5)
DEL PEAK 27(16Q23.1) WILD-TYPE 116 56.1 (11.2)

Figure S11.  Get High-res Image Gene #59: '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 = 562

  • Number of significantly focal cnvs = 68

  • 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)