Correlation between copy number variation genes (focal) and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C14F1NP0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Ovarian Serous Cystadenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C14F1NP0
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 69 arm-level results and 7 clinical features across 562 patients, 9 significant findings detected with Q value < 0.25.

  • Amp Peak 2(1q21.3) cnv correlated to 'AGE'.

  • Amp Peak 14(10p15.3) cnv correlated to 'AGE'.

  • Amp Peak 17(12p13.33) cnv correlated to 'AGE'.

  • Amp Peak 18(12p12.1) cnv correlated to 'AGE'.

  • Amp Peak 25(19q12) cnv correlated to 'AGE'.

  • Amp Peak 26(19q13.2) cnv correlated to 'AGE'.

  • Amp Peak 28(20q11.21) cnv correlated to 'AGE'.

  • Amp Peak 29(20q13.33) cnv correlated to 'AGE'.

  • Del Peak 28(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 69 arm-level results and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		KARNOFSKY
PERFORMANCE
SCORE 		TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 2(1q21 3) 0 (0%) 209 0.291
(1.00) 		4.24e-06
(0.00203) 		0.128
(1.00) 		0.408
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.501
(1.00)
Amp Peak 14(10p15 3) 0 (0%) 323 0.13
(1.00) 		0.000432
(0.205) 		0.154
(1.00) 		0.923
(1.00) 		0.228
(1.00) 		0.578
(1.00) 		0.747
(1.00)
Amp Peak 17(12p13 33) 0 (0%) 247 0.772
(1.00) 		3.54e-07
(0.00017) 		0.756
(1.00) 		0.735
(1.00) 		0.0955
(1.00) 		1
(1.00) 		0.51
(1.00)
Amp Peak 18(12p12 1) 0 (0%) 262 0.0918
(1.00) 		1.23e-08
(5.92e-06) 		0.251
(1.00) 		0.335
(1.00) 		0.0316
(1.00) 		0.601
(1.00) 		1
(1.00)
Amp Peak 25(19q12) 0 (0%) 252 0.602
(1.00) 		1.19e-05
(0.0057) 		0.162
(1.00) 		0.51
(1.00) 		0.104
(1.00) 		1
(1.00) 		1
(1.00)
Amp Peak 26(19q13 2) 0 (0%) 327 0.0201
(1.00) 		3.37e-06
(0.00162) 		0.15
(1.00) 		0.989
(1.00) 		0.639
(1.00) 		0.574
(1.00) 		0.326
(1.00)
Amp Peak 28(20q11 21) 0 (0%) 234 0.104
(1.00) 		7.62e-08
(3.67e-05) 		1
(1.00) 		0.264
(1.00) 		0.0856
(1.00) 		1
(1.00) 		1
(1.00)
Amp Peak 29(20q13 33) 0 (0%) 173 0.331
(1.00) 		9.1e-06
(0.00435) 		1
(1.00) 		0.752
(1.00) 		0.546
(1.00) 		1
(1.00) 		0.0958
(1.00)
Del Peak 28(16q23 1) 0 (0%) 125 0.161
(1.00) 		7.72e-05
(0.0368) 		0.636
(1.00) 		0.0778
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.0885
(1.00)
Amp Peak 1(1p34 3) 0 (0%) 282 0.0333
(1.00) 		0.00962
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.874
(1.00) 		0.123
(1.00) 		0.332
(1.00)
Amp Peak 3(1q42 2) 0 (0%) 256 0.29
(1.00) 		0.000643
(0.304) 		0.252
(1.00) 		0.736
(1.00) 		0.173
(1.00) 		0.594
(1.00) 		0.742
(1.00)
Amp Peak 4(2p23 2) 0 (0%) 327 0.915
(1.00) 		0.0855
(1.00) 		0.762
(1.00) 		0.988
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.501
(1.00)
Amp Peak 5(2q31 2) 0 (0%) 314 0.177
(1.00) 		0.0132
(1.00) 		0.756
(1.00) 		0.693
(1.00) 		0.00661
(1.00) 		0.0853
(1.00) 		0.734
(1.00)
Amp Peak 6(3q26 2) 0 (0%) 96 0.898
(1.00) 		0.000761
(0.359) 		0.527
(1.00) 		0.00131
(0.615) 		0.0553
(1.00) 		1
(1.00) 		0.673
(1.00)
Amp Peak 7(4p16 3) 0 (0%) 407 0.456
(1.00) 		0.644
(1.00) 		0.723
(1.00) 		0.0728
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.481
(1.00)
Amp Peak 8(4q13 3) 0 (0%) 456 0.204
(1.00) 		0.208
(1.00) 		0.571
(1.00) 		0.42
(1.00) 		0.407
(1.00) 		1
(1.00) 		0.28
(1.00)
Amp Peak 9(5p15 33) 0 (0%) 266 0.0538
(1.00) 		0.00274
(1.00) 		0.751
(1.00) 		0.798
(1.00) 		0.292
(1.00) 		0.605
(1.00) 		0.0516
(1.00)
Amp Peak 10(6p22 3) 0 (0%) 277 0.132
(1.00) 		0.00543
(1.00) 		1
(1.00) 		0.545
(1.00) 		0.0489
(1.00) 		0.619
(1.00) 		0.744
(1.00)
Amp Peak 11(7q36 3) 0 (0%) 262 0.291
(1.00) 		0.858
(1.00) 		1
(1.00) 		0.1
(1.00) 		0.741
(1.00) 		0.601
(1.00) 		0.501
(1.00)
Amp Peak 12(8p11 21) 0 (0%) 360 0.335
(1.00) 		0.000534
(0.253) 		0.121
(1.00) 		0.662
(1.00) 		0.317
(1.00) 		0.294
(1.00) 		0.501
(1.00)
Amp Peak 13(8q24 21) 0 (0%) 121 0.547
(1.00) 		0.0995
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.188
(1.00) 		0.518
(1.00) 		0.673
(1.00)
Amp Peak 15(10q22 3) 0 (0%) 388 0.523
(1.00) 		0.221
(1.00) 		0.0934
(1.00) 		0.989
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.719
(1.00)
Amp Peak 16(11q14 1) 0 (0%) 314 0.298
(1.00) 		0.335
(1.00) 		0.256
(1.00) 		0.474
(1.00) 		0.0508
(1.00) 		1
(1.00) 		0.734
(1.00)
Amp Peak 19(14q11 2) 0 (0%) 420 0.752
(1.00) 		0.0651
(1.00) 		0.124
(1.00) 		0.378
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.692
(1.00)
Amp Peak 20(14q32 33) 0 (0%) 412 0.216
(1.00) 		0.0162
(1.00) 		0.711
(1.00) 		0.113
(1.00) 		0.484
(1.00) 		0.175
(1.00) 		1
(1.00)
Amp Peak 21(15q26 3) 0 (0%) 408 0.0716
(1.00) 		0.284
(1.00) 		0.728
(1.00) 		0.42
(1.00) 		0.147
(1.00) 		0.565
(1.00) 		0.734
(1.00)
Amp Peak 22(17q25 3) 0 (0%) 358 0.0217
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.381
(1.00) 		1
(1.00) 		0.186
(1.00)
Amp Peak 23(18q11 2) 0 (0%) 426 0.979
(1.00) 		0.0441
(1.00) 		0.114
(1.00) 		0.18
(1.00) 		0.843
(1.00) 		0.565
(1.00) 		0.712
(1.00)
Amp Peak 24(19p13 12) 0 (0%) 258 0.199
(1.00) 		0.072
(1.00) 		0.461
(1.00) 		0.597
(1.00) 		0.119
(1.00) 		0.596
(1.00) 		0.197
(1.00)
Amp Peak 27(20p13) 0 (0%) 253 0.325
(1.00) 		0.00209
(0.978) 		0.754
(1.00) 		0.11
(1.00) 		0.0202
(1.00) 		1
(1.00) 		0.305
(1.00)
Amp Peak 30(22q12 2) 0 (0%) 474 0.545
(1.00) 		0.0241
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.434
(1.00) 		1
(1.00) 		1
(1.00)
Amp Peak 31(Xp11 23) 0 (0%) 399 0.144
(1.00) 		0.0223
(1.00) 		0.0781
(1.00) 		0.275
(1.00) 		0.364
(1.00) 		0.56
(1.00) 		0.14
(1.00)
Amp Peak 32(Xq28) 0 (0%) 341 0.355
(1.00) 		0.97
(1.00) 		0.77
(1.00) 		0.654
(1.00) 		0.00163
(0.767) 		0.0603
(1.00) 		0.744
(1.00)
Del Peak 1(1p36 11) 0 (0%) 301 0.169
(1.00) 		0.187
(1.00) 		0.751
(1.00) 		0.427
(1.00) 		0.496
(1.00) 		1
(1.00) 		1
(1.00)
Del Peak 2(1q32 3) 0 (0%) 470 0.96
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.423
(1.00) 		0.416
(1.00) 		1
(1.00)
Del Peak 3(2p25 3) 0 (0%) 444 0.922
(1.00) 		0.425
(1.00) 		0.615
(1.00) 		0.875
(1.00) 		0.0602
(1.00) 		0.508
(1.00) 		0.0175
(1.00)
Del Peak 4(2q22 1) 0 (0%) 431 0.25
(1.00) 		0.385
(1.00) 		0.656
(1.00) 		0.595
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.512
(1.00)
Del Peak 5(2q37 3) 0 (0%) 391 0.457
(1.00) 		0.106
(1.00) 		0.359
(1.00) 		0.432
(1.00) 		0.768
(1.00) 		0.221
(1.00) 		0.463
(1.00)
Del Peak 6(3p26 2) 0 (0%) 355 0.792
(1.00) 		0.00246
(1.00) 		0.126
(1.00) 		0.246
(1.00) 		0.136
(1.00) 		0.0495
(1.00) 		0.278
(1.00)
Del Peak 7(4q22 1) 0 (0%) 183 0.51
(1.00) 		0.95
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.0436
(1.00) 		1
(1.00) 		0.481
(1.00)
Del Peak 8(4q34 3) 0 (0%) 155 0.797
(1.00) 		0.36
(1.00) 		0.728
(1.00) 		0.171
(1.00) 		0.796
(1.00) 		0.565
(1.00) 		0.275
(1.00)
Del Peak 9(5q11 2) 0 (0%) 227 0.737
(1.00) 		0.628
(1.00) 		0.767
(1.00) 		0.325
(1.00) 		0.243
(1.00) 		0.568
(1.00) 		0.742
(1.00)
Del Peak 10(5q13 2) 0 (0%) 162 0.261
(1.00) 		0.922
(1.00) 		0.747
(1.00) 		0.216
(1.00) 		0.884
(1.00) 		0.201
(1.00) 		0.742
(1.00)
Del Peak 11(6q27) 0 (0%) 187 0.307
(1.00) 		0.000707
(0.334) 		1
(1.00) 		0.508
(1.00) 		0.371
(1.00) 		1
(1.00) 		0.734
(1.00)
Del Peak 12(7p22 1) 0 (0%) 318 0.09
(1.00) 		0.0291
(1.00) 		0.758
(1.00) 		0.497
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.0862
(1.00)
Del Peak 13(8p23 3) 0 (0%) 185 0.271
(1.00) 		0.0639
(1.00) 		1
(1.00) 		0.95
(1.00) 		0.888
(1.00) 		1
(1.00) 		1
(1.00)
Del Peak 14(8p21 2) 0 (0%) 170 0.672
(1.00) 		0.0645
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.538
(1.00) 		1
(1.00) 		0.734
(1.00)
Del Peak 15(9p24 3) 0 (0%) 309 0.943
(1.00) 		0.025
(1.00) 		0.45
(1.00) 		0.928
(1.00) 		0.397
(1.00) 		0.591
(1.00) 		0.322
(1.00)
Del Peak 16(9q34 13) 0 (0%) 226 0.786
(1.00) 		0.0402
(1.00) 		0.767
(1.00) 		0.623
(1.00) 		0.859
(1.00) 		0.277
(1.00) 		0.326
(1.00)
Del Peak 17(10p15 3) 0 (0%) 444 0.336
(1.00) 		0.83
(1.00) 		0.608
(1.00) 		0.72
(1.00) 		0.392
(1.00) 		0.508
(1.00) 		1
(1.00)
Del Peak 18(10q23 31) 0 (0%) 343 0.328
(1.00) 		0.972
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.625
(1.00) 		0.563
(1.00) 		0.463
(1.00)
Del Peak 19(10q26 3) 0 (0%) 373 0.0829
(1.00) 		0.842
(1.00) 		0.8
(1.00) 		0.77
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.734
(1.00)
Del Peak 20(11p15 5) 0 (0%) 230 0.0509
(1.00) 		0.563
(1.00) 		0.0267
(1.00) 		0.267
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.512
(1.00)
Del Peak 21(11q25) 0 (0%) 369 0.598
(1.00) 		0.0797
(1.00) 		0.225
(1.00) 		0.631
(1.00) 		0.0759
(1.00) 		0.272
(1.00) 		0.267
(1.00)
Del Peak 22(12q24 33) 0 (0%) 351 0.655
(1.00) 		0.112
(1.00) 		0.13
(1.00) 		0.652
(1.00) 		0.539
(1.00) 		0.295
(1.00) 		0.0838
(1.00)
Del Peak 23(13q14 2) 0 (0%) 213 0.0714
(1.00) 		0.561
(1.00) 		0.777
(1.00) 		0.592
(1.00) 		0.747
(1.00) 		0.56
(1.00) 		0.189
(1.00)
Del Peak 24(14q23 3) 0 (0%) 267 0.453
(1.00) 		0.589
(1.00) 		0.475
(1.00) 		0.0123
(1.00) 		0.384
(1.00) 		0.107
(1.00) 		0.306
(1.00)
Del Peak 25(15q15 1) 0 (0%) 209 0.664
(1.00) 		0.00579
(1.00) 		0.411
(1.00) 		0.253
(1.00) 		0.0296
(1.00) 		0.298
(1.00) 		0.742
(1.00)
Del Peak 26(16p13 3) 0 (0%) 263 0.886
(1.00) 		0.883
(1.00) 		0.751
(1.00) 		0.578
(1.00) 		0.217
(1.00) 		0.602
(1.00) 		0.512
(1.00)
Del Peak 27(16q22 1) 0 (0%) 115 0.645
(1.00) 		0.00497
(1.00) 		0.193
(1.00) 		0.275
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.231
(1.00)
Del Peak 29(17p12) 0 (0%) 87 0.797
(1.00) 		0.982
(1.00) 		0.493
(1.00) 		0.73
(1.00) 		0.0127
(1.00) 		1
(1.00) 		0.712
(1.00)
Del Peak 30(17q11 2) 0 (0%) 102 0.708
(1.00) 		0.0331
(1.00) 		0.0666
(1.00) 		0.686
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.734
(1.00)
Del Peak 31(18q23) 0 (0%) 194 0.673
(1.00) 		0.454
(1.00) 		0.225
(1.00) 		0.544
(1.00) 		0.708
(1.00) 		1
(1.00) 		1
(1.00)
Del Peak 32(19p13 3) 0 (0%) 67 0.19
(1.00) 		0.0164
(1.00) 		1
(1.00) 		0.00833
(1.00) 		0.0647
(1.00) 		1
(1.00) 		0.692
(1.00)
Del Peak 33(19q13 33) 0 (0%) 271 0.603
(1.00) 		0.355
(1.00) 		1
(1.00) 		0.311
(1.00) 		0.374
(1.00) 		0.25
(1.00) 		1
(1.00)
Del Peak 34(19q13 43) 0 (0%) 286 0.389
(1.00) 		0.0316
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.52
(1.00)
Del Peak 35(21q22 3) 0 (0%) 345 0.584
(1.00) 		0.35
(1.00) 		0.774
(1.00) 		0.665
(1.00) 		0.124
(1.00) 		1
(1.00) 		1
(1.00)
Del Peak 36(22q13 32) 0 (0%) 75 0.843
(1.00) 		0.901
(1.00) 		0.443
(1.00) 		0.752
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.596
(1.00)
Del Peak 37(Xp21 1) 0 (0%) 202 0.838
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.987
(1.00) 		0.682
(1.00) 		0.556
(1.00) 		0.742
(1.00)
'Amp Peak 2(1q21.3)' versus 'AGE'

P value = 4.24e-06 (t-test), Q value = 0.002

Table S1.  Gene #2: 'Amp Peak 2(1q21.3)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 2(1Q21.3) CNV 341 61.6 (11.0)
AMP PEAK 2(1Q21.3) WILD-TYPE 200 56.8 (12.0)

Figure S1.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Clinical Feature #2: 'AGE'

'Amp Peak 14(10p15.3)' versus 'AGE'

P value = 0.000432 (t-test), Q value = 0.21

Table S2.  Gene #14: 'Amp Peak 14(10p15.3)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 14(10P15.3) CNV 233 61.8 (11.2)
AMP PEAK 14(10P15.3) WILD-TYPE 308 58.3 (11.7)

Figure S2.  Get High-res Image Gene #14: 'Amp Peak 14(10p15.3)' versus Clinical Feature #2: 'AGE'

'Amp Peak 17(12p13.33)' versus 'AGE'

P value = 3.54e-07 (t-test), Q value = 0.00017

Table S3.  Gene #17: 'Amp Peak 17(12p13.33)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 17(12P13.33) CNV 303 62.1 (10.8)
AMP PEAK 17(12P13.33) WILD-TYPE 238 56.9 (12.0)

Figure S3.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Clinical Feature #2: 'AGE'

'Amp Peak 18(12p12.1)' versus 'AGE'

P value = 1.23e-08 (t-test), Q value = 5.9e-06

Table S4.  Gene #18: 'Amp Peak 18(12p12.1)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 18(12P12.1) CNV 286 62.5 (11.2)
AMP PEAK 18(12P12.1) WILD-TYPE 255 56.8 (11.4)

Figure S4.  Get High-res Image Gene #18: 'Amp Peak 18(12p12.1)' versus Clinical Feature #2: 'AGE'

'Amp Peak 25(19q12)' versus 'AGE'

P value = 1.19e-05 (t-test), Q value = 0.0057

Table S5.  Gene #25: 'Amp Peak 25(19q12)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 25(19Q12) CNV 300 61.8 (11.1)
AMP PEAK 25(19Q12) WILD-TYPE 241 57.4 (11.7)

Figure S5.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Clinical Feature #2: 'AGE'

'Amp Peak 26(19q13.2)' versus 'AGE'

P value = 3.37e-06 (t-test), Q value = 0.0016

Table S6.  Gene #26: 'Amp Peak 26(19q13.2)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 26(19Q13.2) CNV 228 62.5 (11.2)
AMP PEAK 26(19Q13.2) WILD-TYPE 313 57.8 (11.5)

Figure S6.  Get High-res Image Gene #26: 'Amp Peak 26(19q13.2)' versus Clinical Feature #2: 'AGE'

'Amp Peak 28(20q11.21)' versus 'AGE'

P value = 7.62e-08 (t-test), Q value = 3.7e-05

Table S7.  Gene #28: 'Amp Peak 28(20q11.21)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 28(20Q11.21) CNV 315 62.0 (11.5)
AMP PEAK 28(20Q11.21) WILD-TYPE 226 56.7 (11.0)

Figure S7.  Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Clinical Feature #2: 'AGE'

'Amp Peak 29(20q13.33)' versus 'AGE'

P value = 9.1e-06 (t-test), Q value = 0.0044

Table S8.  Gene #29: 'Amp Peak 29(20q13.33)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 29(20Q13.33) CNV 376 61.2 (11.5)
AMP PEAK 29(20Q13.33) WILD-TYPE 165 56.5 (11.1)

Figure S8.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Clinical Feature #2: 'AGE'

'Del Peak 28(16q23.1)' versus 'AGE'

P value = 7.72e-05 (t-test), Q value = 0.037

Table S9.  Gene #60: 'Del Peak 28(16q23.1)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
DEL PEAK 28(16Q23.1) CNV 423 60.8 (11.5)
DEL PEAK 28(16Q23.1) WILD-TYPE 118 56.1 (11.2)

Figure S9.  Get High-res Image Gene #60: 'Del Peak 28(16q23.1)' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 562

  • Number of significantly arm-level cnvs = 69

  • Number of selected clinical features = 7

  • 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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