Correlation between copy number variation genes (focal) and selected clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1W95775
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 variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1W95775
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 84 arm-level results and 13 clinical features across 345 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 84 arm-level results and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		COMPLETENESS
OF
RESECTION 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test Chi-square test Fisher's exact test t-test Chi-square test
Amp Peak 1(1p34 2) 0 (0%) 283 0.287
(1.00) 		0.784
(1.00) 		0.103
(1.00) 		0.939
(1.00) 		0.0684
(1.00) 		0.458
(1.00) 		0.239
(1.00) 		0.422
(1.00) 		0.24
(1.00) 		0.761
(1.00) 		1
(1.00) 		0.157
(1.00)
Amp Peak 2(1q21 2) 0 (0%) 160 0.0782
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.718
(1.00) 		0.172
(1.00) 		0.395
(1.00) 		0.629
(1.00) 		0.293
(1.00) 		0.352
(1.00) 		0.904
(1.00) 		0.564
(1.00) 		0.549
(1.00)
Amp Peak 3(2p16 1) 0 (0%) 153 0.993
(1.00) 		0.382
(1.00) 		0.129
(1.00) 		0.496
(1.00) 		0.209
(1.00) 		0.559
(1.00) 		0.231
(1.00) 		0.0334
(1.00) 		0.68
(1.00) 		0.0335
(1.00) 		0.466
(1.00) 		0.638
(1.00)
Amp Peak 4(2q31 2) 0 (0%) 224 0.809
(1.00) 		0.233
(1.00) 		0.189
(1.00) 		0.856
(1.00) 		0.231
(1.00) 		0.552
(1.00) 		0.315
(1.00) 		0.0635
(1.00) 		0.569
(1.00) 		0.758
(1.00) 		0.0729
(1.00) 		0.468
(1.00)
Amp Peak 5(3p11 1) 0 (0%) 276 0.76
(1.00) 		0.438
(1.00) 		0.64
(1.00) 		0.835
(1.00) 		1
(1.00) 		0.069
(1.00) 		0.945
(1.00) 		0.682
(1.00) 		0.531
(1.00) 		0.496
(1.00) 		0.283
(1.00) 		0.106
(1.00)
Amp Peak 6(3q26 33) 0 (0%) 29 0.00822
(1.00) 		0.538
(1.00) 		0.177
(1.00) 		0.859
(1.00) 		0.318
(1.00) 		0.609
(1.00) 		0.284
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.152
(1.00) 		0.839
(1.00) 		0.448
(1.00)
Amp Peak 7(4q12) 0 (0%) 265 0.336
(1.00) 		0.28
(1.00) 		0.881
(1.00) 		0.32
(1.00) 		0.535
(1.00) 		0.74
(1.00) 		0.5
(1.00) 		0.172
(1.00) 		0.602
(1.00) 		0.604
(1.00) 		0.392
(1.00) 		0.199
(1.00)
Amp Peak 8(5p15 33) 0 (0%) 69 0.739
(1.00) 		0.88
(1.00) 		0.753
(1.00) 		0.925
(1.00) 		0.47
(1.00) 		0.713
(1.00) 		0.773
(1.00) 		0.59
(1.00) 		0.531
(1.00) 		0.0231
(1.00) 		0.566
(1.00) 		0.564
(1.00)
Amp Peak 9(5p12) 0 (0%) 114 0.763
(1.00) 		0.101
(1.00) 		0.593
(1.00) 		0.752
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.963
(1.00) 		1
(1.00) 		0.238
(1.00) 		0.776
(1.00) 		0.83
(1.00)
Amp Peak 10(6p12 1) 0 (0%) 233 0.783
(1.00) 		0.605
(1.00) 		0.893
(1.00) 		0.799
(1.00) 		0.363
(1.00) 		0.536
(1.00) 		0.323
(1.00) 		0.517
(1.00) 		0.165
(1.00) 		0.449
(1.00) 		0.671
(1.00) 		0.374
(1.00)
Amp Peak 11(7p11 2) 0 (0%) 170 0.147
(1.00) 		0.495
(1.00) 		0.316
(1.00) 		0.542
(1.00) 		0.68
(1.00) 		0.569
(1.00) 		0.101
(1.00) 		0.36
(1.00) 		0.488
(1.00) 		0.112
(1.00) 		0.576
(1.00) 		0.0251
(1.00)
Amp Peak 12(7q21 2) 0 (0%) 156 0.354
(1.00) 		0.438
(1.00) 		0.206
(1.00) 		0.0155
(1.00) 		0.92
(1.00) 		0.149
(1.00) 		0.667
(1.00) 		0.598
(1.00) 		0.452
(1.00) 		0.0437
(1.00) 		0.369
(1.00) 		0.324
(1.00)
Amp Peak 13(8p11 23) 0 (0%) 178 0.0967
(1.00) 		0.316
(1.00) 		0.0783
(1.00) 		0.0599
(1.00) 		0.557
(1.00) 		0.564
(1.00) 		0.81
(1.00) 		0.182
(1.00) 		0.649
(1.00) 		0.974
(1.00) 		0.0012
(1.00) 		0.27
(1.00)
Amp Peak 14(8q24 21) 0 (0%) 100 0.735
(1.00) 		0.844
(1.00) 		0.409
(1.00) 		0.496
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.869
(1.00) 		0.817
(1.00) 		0.19
(1.00) 		0.123
(1.00) 		0.0566
(1.00) 		0.111
(1.00)
Amp Peak 15(9p24 1) 0 (0%) 282 0.323
(1.00) 		0.489
(1.00) 		0.748
(1.00) 		0.303
(1.00) 		0.015
(1.00) 		0.134
(1.00) 		0.452
(1.00) 		0.324
(1.00) 		0.585
(1.00) 		0.738
(1.00) 		0.802
(1.00) 		0.129
(1.00)
Amp Peak 16(9p13 3) 0 (0%) 251 0.164
(1.00) 		0.385
(1.00) 		0.572
(1.00) 		0.146
(1.00) 		0.0756
(1.00) 		0.524
(1.00) 		0.558
(1.00) 		0.668
(1.00) 		0.757
(1.00) 		0.6
(1.00) 		0.11
(1.00) 		0.14
(1.00)
Amp Peak 17(11q13 3) 0 (0%) 218 0.494
(1.00) 		0.7
(1.00) 		0.365
(1.00) 		0.154
(1.00) 		1
(1.00) 		0.223
(1.00) 		0.635
(1.00) 		0.162
(1.00) 		0.844
(1.00) 		0.854
(1.00) 		0.951
(1.00) 		0.341
(1.00)
Amp Peak 18(12p13 33) 0 (0%) 169 0.977
(1.00) 		0.696
(1.00) 		0.0436
(1.00) 		0.315
(1.00) 		0.928
(1.00) 		0.567
(1.00) 		0.958
(1.00) 		0.579
(1.00) 		0.401
(1.00) 		0.419
(1.00) 		0.852
(1.00) 		0.414
(1.00)
Amp Peak 19(12q15) 0 (0%) 217 0.641
(1.00) 		0.577
(1.00) 		0.0901
(1.00) 		0.932
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.788
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.753
(1.00) 		0.483
(1.00)
Amp Peak 20(13q34) 0 (0%) 284 0.271
(1.00) 		0.0957
(1.00) 		0.098
(1.00) 		0.272
(1.00) 		0.0217
(1.00) 		1
(1.00) 		0.06
(1.00) 		0.175
(1.00) 		0.604
(1.00) 		0.369
(1.00) 		0.256
(1.00) 		0.8
(1.00)
Amp Peak 21(14q13 3) 0 (0%) 237 0.177
(1.00) 		0.00227
(1.00) 		0.892
(1.00) 		0.727
(1.00) 		0.58
(1.00) 		0.76
(1.00) 		0.615
(1.00) 		0.539
(1.00) 		0.33
(1.00) 		0.361
(1.00) 		0.449
(1.00) 		0.183
(1.00)
Amp Peak 22(15q26 3) 0 (0%) 224 0.846
(1.00) 		0.334
(1.00) 		0.432
(1.00) 		0.694
(1.00) 		0.393
(1.00) 		0.552
(1.00) 		0.448
(1.00) 		0.926
(1.00) 		0.0824
(1.00) 		0.71
(1.00) 		0.885
(1.00) 		0.774
(1.00)
Amp Peak 23(17q25 1) 0 (0%) 181 0.92
(1.00) 		0.451
(1.00) 		0.0229
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.0756
(1.00) 		0.841
(1.00) 		0.0141
(1.00) 		0.809
(1.00) 		0.106
(1.00) 		0.388
(1.00) 		0.384
(1.00)
Amp Peak 24(18p11 32) 0 (0%) 225 0.425
(1.00) 		0.121
(1.00) 		0.146
(1.00) 		0.784
(1.00) 		0.474
(1.00) 		0.355
(1.00) 		0.536
(1.00) 		0.442
(1.00) 		0.645
(1.00) 		0.495
(1.00) 		0.441
(1.00) 		0.584
(1.00)
Amp Peak 25(18q11 2) 0 (0%) 231 0.888
(1.00) 		0.826
(1.00) 		0.894
(1.00) 		0.582
(1.00) 		0.737
(1.00) 		0.541
(1.00) 		0.332
(1.00) 		0.793
(1.00) 		0.821
(1.00) 		0.353
(1.00) 		0.712
(1.00) 		0.632
(1.00)
Amp Peak 26(19q12) 0 (0%) 199 0.249
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.319
(1.00) 		0.0332
(1.00) 		0.479
(1.00) 		0.163
(1.00) 		0.729
(1.00) 		0.0498
(1.00) 		0.934
(1.00) 		0.694
(1.00)
Amp Peak 27(19q13 2) 0 (0%) 196 0.677
(1.00) 		0.363
(1.00) 		0.526
(1.00) 		0.19
(1.00) 		0.184
(1.00) 		0.376
(1.00) 		0.00684
(1.00) 		0.0124
(1.00) 		0.879
(1.00) 		0.364
(1.00) 		0.745
(1.00) 		0.87
(1.00)
Amp Peak 28(20p12 2) 0 (0%) 156 0.334
(1.00) 		0.312
(1.00) 		0.129
(1.00) 		0.399
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.555
(1.00) 		0.737
(1.00) 		0.603
(1.00) 		0.681
(1.00) 		0.851
(1.00) 		0.281
(1.00)
Amp Peak 29(20q11 21) 0 (0%) 138 0.413
(1.00) 		0.23
(1.00) 		0.00305
(1.00) 		0.851
(1.00) 		0.065
(1.00) 		0.769
(1.00) 		0.392
(1.00) 		0.177
(1.00) 		0.486
(1.00) 		0.0712
(1.00) 		0.802
(1.00) 		0.454
(1.00)
Amp Peak 30(22q11 21) 0 (0%) 173 0.881
(1.00) 		0.434
(1.00) 		0.45
(1.00) 		0.803
(1.00) 		0.107
(1.00) 		0.379
(1.00) 		0.613
(1.00) 		0.25
(1.00) 		0.241
(1.00) 		0.0891
(1.00) 		0.0341
(1.00) 		0.0467
(1.00)
Amp Peak 31(Xq28) 0 (0%) 254 0.328
(1.00) 		0.402
(1.00) 		0.476
(1.00) 		0.187
(1.00) 		0.757
(1.00) 		0.739
(1.00) 		0.374
(1.00) 		0.157
(1.00) 		0.746
(1.00) 		0.692
(1.00) 		0.253
(1.00) 		0.199
(1.00)
Del Peak 1(1p36 22) 0 (0%) 193 0.672
(1.00) 		0.236
(1.00) 		0.0316
(1.00) 		0.757
(1.00) 		0.676
(1.00) 		0.771
(1.00) 		0.441
(1.00) 		0.173
(1.00) 		0.522
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.425
(1.00)
Del Peak 2(1p13 1) 0 (0%) 194 0.816
(1.00) 		0.0464
(1.00) 		0.447
(1.00) 		0.234
(1.00) 		0.918
(1.00) 		0.242
(1.00) 		0.432
(1.00) 		0.041
(1.00) 		0.0663
(1.00) 		0.829
(1.00) 		0.967
(1.00) 		0.758
(1.00)
Del Peak 3(2p25 3) 0 (0%) 313 0.407
(1.00) 		0.0378
(1.00) 		0.384
(1.00) 		0.882
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.131
(1.00) 		0.643
(1.00) 		0.432
(1.00) 		0.171
(1.00) 		0.787
(1.00) 		0.0846
(1.00)
Del Peak 4(2q22 1) 0 (0%) 255 0.875
(1.00) 		0.00161
(1.00) 		0.319
(1.00) 		0.308
(1.00) 		0.0776
(1.00) 		0.197
(1.00) 		0.756
(1.00) 		0.00291
(1.00) 		0.872
(1.00) 		0.043
(1.00) 		0.372
(1.00) 		0.278
(1.00)
Del Peak 5(2q36 2) 0 (0%) 232 0.182
(1.00) 		0.00468
(1.00) 		0.423
(1.00) 		0.601
(1.00) 		0.906
(1.00) 		0.538
(1.00) 		0.188
(1.00) 		0.00566
(1.00) 		0.79
(1.00) 		0.389
(1.00) 		0.928
(1.00) 		0.674
(1.00)
Del Peak 6(3p25 3) 0 (0%) 69 0.356
(1.00) 		0.178
(1.00) 		1
(1.00) 		0.395
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.679
(1.00) 		0.704
(1.00) 		0.7
(1.00) 		0.155
(1.00) 		0.741
(1.00) 		0.196
(1.00)
Del Peak 7(3p13) 0 (0%) 49 0.558
(1.00) 		0.0974
(1.00) 		0.718
(1.00) 		0.12
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.901
(1.00) 		0.788
(1.00) 		0.513
(1.00) 		0.203
(1.00) 		0.0261
(1.00)
Del Peak 8(3p12 3) 0 (0%) 57 0.255
(1.00) 		0.0527
(1.00) 		0.735
(1.00) 		0.197
(1.00) 		0.474
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.781
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.362
(1.00) 		0.0648
(1.00)
Del Peak 9(3q11 1) 0 (0%) 292 0.0422
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.14
(1.00) 		0.353
(1.00) 		0.701
(1.00) 		0.335
(1.00) 		0.538
(1.00) 		0.157
(1.00) 		0.615
(1.00) 		0.427
(1.00) 		0.42
(1.00)
Del Peak 10(4p15 2) 0 (0%) 137 0.148
(1.00) 		0.331
(1.00) 		0.609
(1.00) 		0.52
(1.00) 		1
(1.00) 		0.376
(1.00) 		0.837
(1.00) 		0.829
(1.00) 		0.577
(1.00) 		0.793
(1.00) 		0.446
(1.00) 		0.377
(1.00)
Del Peak 11(4q22 1) 0 (0%) 152 0.0307
(1.00) 		0.321
(1.00) 		0.165
(1.00) 		0.742
(1.00) 		0.918
(1.00) 		0.0738
(1.00) 		0.153
(1.00) 		0.338
(1.00) 		0.518
(1.00) 		0.571
(1.00) 		0.523
(1.00) 		0.177
(1.00)
Del Peak 12(4q32 3) 0 (0%) 128 0.256
(1.00) 		0.279
(1.00) 		0.241
(1.00) 		0.922
(1.00) 		0.642
(1.00) 		0.546
(1.00) 		0.0163
(1.00) 		0.857
(1.00) 		0.849
(1.00) 		0.439
(1.00) 		0.828
(1.00) 		0.137
(1.00)
Del Peak 13(4q35 2) 0 (0%) 124 0.76
(1.00) 		0.658
(1.00) 		0.896
(1.00) 		0.7
(1.00) 		0.581
(1.00) 		0.548
(1.00) 		0.0436
(1.00) 		0.743
(1.00) 		0.713
(1.00) 		0.367
(1.00) 		0.728
(1.00) 		0.14
(1.00)
Del Peak 14(5q11 2) 0 (0%) 92 0.451
(1.00) 		0.203
(1.00) 		0.319
(1.00) 		0.928
(1.00) 		0.321
(1.00) 		0.527
(1.00) 		0.438
(1.00) 		0.253
(1.00) 		0.732
(1.00) 		0.399
(1.00) 		0.147
(1.00) 		0.8
(1.00)
Del Peak 15(5q31 1) 0 (0%) 82 0.306
(1.00) 		0.918
(1.00) 		0.659
(1.00) 		0.494
(1.00) 		0.362
(1.00) 		0.738
(1.00) 		0.773
(1.00) 		0.154
(1.00) 		0.698
(1.00) 		0.662
(1.00) 		0.199
(1.00) 		0.602
(1.00)
Del Peak 16(6p25 3) 0 (0%) 257 0.135
(1.00) 		0.961
(1.00) 		0.0836
(1.00) 		0.524
(1.00) 		0.744
(1.00) 		0.738
(1.00) 		0.981
(1.00) 		0.505
(1.00) 		0.668
(1.00) 		0.615
(1.00) 		0.0639
(1.00) 		0.348
(1.00)
Del Peak 17(6q22 31) 0 (0%) 257 0.74
(1.00) 		0.784
(1.00) 		0.389
(1.00) 		0.244
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.0742
(1.00) 		0.744
(1.00) 		0.657
(1.00) 		0.324
(1.00) 		0.107
(1.00)
Del Peak 18(6q26) 0 (0%) 249 0.331
(1.00) 		0.519
(1.00) 		0.673
(1.00) 		0.156
(1.00) 		0.777
(1.00) 		0.744
(1.00) 		0.8
(1.00) 		0.319
(1.00) 		0.204
(1.00) 		0.712
(1.00) 		0.728
(1.00) 		0.365
(1.00)
Del Peak 19(7q11 22) 0 (0%) 312 0.317
(1.00) 		0.518
(1.00) 		0.67
(1.00) 		0.588
(1.00) 		0.639
(1.00) 		0.321
(1.00) 		0.638
(1.00) 		0.752
(1.00) 		0.725
(1.00) 		0.815
(1.00) 		0.56
(1.00) 		0.693
(1.00)
Del Peak 20(7q36 3) 0 (0%) 272 0.645
(1.00) 		0.149
(1.00) 		0.647
(1.00) 		0.234
(1.00) 		0.826
(1.00) 		0.722
(1.00) 		0.235
(1.00) 		0.022
(1.00) 		0.864
(1.00) 		0.349
(1.00) 		0.511
(1.00) 		0.525
(1.00)
Del Peak 21(8p23 2) 0 (0%) 103 0.99
(1.00) 		0.0156
(1.00) 		1
(1.00) 		0.131
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.117
(1.00) 		0.577
(1.00) 		0.0264
(1.00) 		0.44
(1.00) 		0.382
(1.00) 		0.0466
(1.00)
Del Peak 22(9p23) 0 (0%) 123 0.594
(1.00) 		0.299
(1.00) 		0.114
(1.00) 		0.582
(1.00) 		0.238
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.487
(1.00) 		0.888
(1.00) 		0.587
(1.00) 		0.779
(1.00) 		0.413
(1.00)
Del Peak 23(9p21 3) 0 (0%) 87 0.622
(1.00) 		0.412
(1.00) 		0.0436
(1.00) 		0.314
(1.00) 		0.0359
(1.00) 		0.507
(1.00) 		0.381
(1.00) 		0.329
(1.00) 		0.91
(1.00) 		0.328
(1.00) 		0.965
(1.00) 		0.367
(1.00)
Del Peak 24(9p21 1) 0 (0%) 125 0.343
(1.00) 		0.237
(1.00) 		0.149
(1.00) 		0.866
(1.00) 		0.295
(1.00) 		0.364
(1.00) 		0.123
(1.00) 		0.32
(1.00) 		0.316
(1.00) 		0.653
(1.00) 		0.724
(1.00) 		0.157
(1.00)
Del Peak 25(9q21 11) 0 (0%) 177 0.741
(1.00) 		0.0102
(1.00) 		0.259
(1.00) 		0.938
(1.00) 		0.522
(1.00) 		0.381
(1.00) 		0.491
(1.00) 		0.167
(1.00) 		0.213
(1.00) 		0.962
(1.00) 		0.897
(1.00) 		0.627
(1.00)
Del Peak 26(10p15 3) 0 (0%) 185 0.229
(1.00) 		0.661
(1.00) 		0.312
(1.00) 		0.774
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.0765
(1.00) 		0.805
(1.00) 		0.224
(1.00) 		0.668
(1.00) 		0.841
(1.00) 		0.493
(1.00)
Del Peak 27(10p15 1) 0 (0%) 196 0.133
(1.00) 		0.877
(1.00) 		0.526
(1.00) 		0.502
(1.00) 		0.852
(1.00) 		0.769
(1.00) 		0.104
(1.00) 		0.658
(1.00) 		0.272
(1.00) 		0.576
(1.00) 		0.9
(1.00) 		0.571
(1.00)
Del Peak 28(10q23 31) 0 (0%) 168 0.348
(1.00) 		0.725
(1.00) 		0.259
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.566
(1.00) 		0.794
(1.00) 		0.97
(1.00) 		0.119
(1.00) 		0.635
(1.00) 		0.368
(1.00) 		0.324
(1.00)
Del Peak 29(11p15 5) 0 (0%) 183 0.23
(1.00) 		0.491
(1.00) 		0.377
(1.00) 		0.277
(1.00) 		0.787
(1.00) 		0.559
(1.00) 		0.781
(1.00) 		0.846
(1.00) 		0.0949
(1.00) 		0.53
(1.00) 		0.788
(1.00) 		0.144
(1.00)
Del Peak 30(11q22 1) 0 (0%) 240 0.682
(1.00) 		0.547
(1.00) 		0.101
(1.00) 		0.694
(1.00) 		0.375
(1.00) 		0.76
(1.00) 		0.728
(1.00) 		0.841
(1.00) 		0.247
(1.00) 		0.0712
(1.00) 		0.879
(1.00) 		0.925
(1.00)
Del Peak 31(11q25) 0 (0%) 211 0.702
(1.00) 		0.954
(1.00) 		0.197
(1.00) 		0.632
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.711
(1.00) 		0.73
(1.00) 		0.365
(1.00) 		0.147
(1.00) 		0.626
(1.00) 		0.935
(1.00)
Del Peak 32(12q24 32) 0 (0%) 282 0.156
(1.00) 		0.475
(1.00) 		0.104
(1.00) 		0.882
(1.00) 		0.0715
(1.00) 		0.702
(1.00) 		0.0636
(1.00) 		0.981
(1.00) 		0.416
(1.00) 		0.619
(1.00) 		0.702
(1.00) 		0.396
(1.00)
Del Peak 33(13q12 11) 0 (0%) 112 0.363
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.733
(1.00) 		0.758
(1.00) 		0.542
(1.00) 		0.123
(1.00) 		0.203
(1.00) 		0.644
(1.00) 		0.897
(1.00) 		0.252
(1.00)
Del Peak 34(13q14 2) 0 (0%) 107 0.947
(1.00) 		0.423
(1.00) 		0.0769
(1.00) 		0.549
(1.00) 		0.281
(1.00) 		0.761
(1.00) 		0.684
(1.00) 		0.559
(1.00) 		0.125
(1.00) 		0.804
(1.00) 		0.888
(1.00) 		0.406
(1.00)
Del Peak 35(14q11 2) 0 (0%) 219 0.0999
(1.00) 		0.428
(1.00) 		0.896
(1.00) 		0.522
(1.00) 		0.451
(1.00) 		0.764
(1.00) 		0.669
(1.00) 		0.489
(1.00) 		0.364
(1.00) 		0.925
(1.00) 		1
(1.00) 		0.447
(1.00)
Del Peak 36(15q12) 0 (0%) 226 0.436
(1.00) 		0.0293
(1.00) 		0.185
(1.00) 		0.487
(1.00) 		0.514
(1.00) 		0.353
(1.00) 		0.253
(1.00) 		0.191
(1.00) 		0.545
(1.00) 		0.0345
(1.00) 		0.353
(1.00) 		0.0762
(1.00)
Del Peak 37(15q21 1) 0 (0%) 232 0.674
(1.00) 		0.0626
(1.00) 		0.503
(1.00) 		0.205
(1.00) 		0.294
(1.00) 		0.218
(1.00) 		0.388
(1.00) 		0.296
(1.00) 		0.622
(1.00) 		0.00442
(1.00) 		0.532
(1.00) 		0.0188
(1.00)
Del Peak 38(16p13 3) 0 (0%) 221 0.13
(1.00) 		0.188
(1.00) 		0.432
(1.00) 		0.691
(1.00) 		0.0577
(1.00) 		1
(1.00) 		0.299
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.421
(1.00) 		0.651
(1.00)
Del Peak 39(16q23 1) 0 (0%) 208 0.249
(1.00) 		0.728
(1.00) 		0.201
(1.00) 		0.833
(1.00) 		0.838
(1.00) 		0.552
(1.00) 		0.202
(1.00) 		0.258
(1.00) 		0.181
(1.00) 		0.642
(1.00) 		0.615
(1.00) 		0.666
(1.00)
Del Peak 40(17p11 2) 0 (0%) 166 0.407
(1.00) 		0.22
(1.00) 		0.316
(1.00) 		0.138
(1.00) 		0.238
(1.00) 		0.0369
(1.00) 		0.000474
(0.477) 		0.0569
(1.00) 		0.913
(1.00) 		0.558
(1.00) 		0.349
(1.00) 		0.846
(1.00)
Del Peak 41(17q11 2) 0 (0%) 260 0.997
(1.00) 		0.187
(1.00) 		0.663
(1.00) 		0.23
(1.00) 		0.377
(1.00) 		0.737
(1.00) 		0.235
(1.00) 		0.418
(1.00) 		0.51
(1.00) 		0.0571
(1.00) 		0.966
(1.00) 		0.431
(1.00)
Del Peak 42(17q25 3) 0 (0%) 274 0.401
(1.00) 		0.48
(1.00) 		0.64
(1.00) 		0.262
(1.00) 		0.819
(1.00) 		0.717
(1.00) 		0.694
(1.00) 		0.155
(1.00) 		0.43
(1.00) 		0.628
(1.00) 		0.962
(1.00) 		0.805
(1.00)
Del Peak 43(18q23) 0 (0%) 186 0.274
(1.00) 		0.0518
(1.00) 		0.0432
(1.00) 		0.456
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.864
(1.00) 		0.24
(1.00) 		0.913
(1.00) 		0.445
(1.00) 		0.296
(1.00) 		0.798
(1.00)
Del Peak 44(19p13 3) 0 (0%) 190 0.263
(1.00) 		0.783
(1.00) 		0.448
(1.00) 		0.0679
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.342
(1.00) 		0.337
(1.00) 		0.135
(1.00) 		0.875
(1.00) 		0.137
(1.00)
Del Peak 45(19q13 33) 0 (0%) 254 0.43
(1.00) 		0.0291
(1.00) 		0.476
(1.00) 		0.206
(1.00) 		0.504
(1.00) 		0.524
(1.00) 		0.0358
(1.00) 		0.00189
(1.00) 		0.636
(1.00) 		0.353
(1.00) 		0.199
(1.00) 		0.687
(1.00)
Del Peak 46(19q13 43) 0 (0%) 255 0.251
(1.00) 		0.148
(1.00) 		0.0627
(1.00) 		0.137
(1.00) 		0.162
(1.00) 		0.519
(1.00) 		0.0477
(1.00) 		0.112
(1.00) 		0.744
(1.00) 		0.671
(1.00) 		0.175
(1.00) 		0.613
(1.00)
Del Peak 47(21q21 1) 0 (0%) 178 0.304
(1.00) 		0.735
(1.00) 		0.0783
(1.00) 		0.858
(1.00) 		0.927
(1.00) 		0.382
(1.00) 		0.843
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.773
(1.00) 		0.948
(1.00)
Del Peak 48(21q22 3) 0 (0%) 149 0.819
(1.00) 		0.579
(1.00) 		0.0111
(1.00) 		0.821
(1.00) 		0.622
(1.00) 		0.769
(1.00) 		0.833
(1.00) 		0.588
(1.00) 		0.35
(1.00) 		0.939
(1.00) 		0.756
(1.00) 		0.592
(1.00)
Del Peak 49(22q11 21) 0 (0%) 285 0.939
(1.00) 		0.0575
(1.00) 		0.62
(1.00) 		0.976
(1.00) 		0.234
(1.00) 		0.234
(1.00) 		0.896
(1.00) 		0.316
(1.00) 		0.125
(1.00) 		0.284
(1.00) 		0.221
(1.00) 		0.364
(1.00)
Del Peak 50(22q13 32) 0 (0%) 265 0.366
(1.00) 		0.0125
(1.00) 		0.296
(1.00) 		0.274
(1.00) 		0.0143
(1.00) 		0.484
(1.00) 		0.527
(1.00) 		0.339
(1.00) 		0.296
(1.00) 		0.0829
(1.00) 		0.773
(1.00) 		0.693
(1.00)
Del Peak 51(Xp22 2) 0 (0%) 238 0.461
(1.00) 		0.233
(1.00) 		0.222
(1.00) 		0.091
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.0746
(1.00) 		0.803
(1.00) 		0.05
(1.00) 		0.775
(1.00) 		0.359
(1.00)
Del Peak 52(Xp11 3) 0 (0%) 240 0.915
(1.00) 		0.597
(1.00) 		0.413
(1.00) 		0.0064
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.15
(1.00) 		0.402
(1.00) 		0.126
(1.00) 		0.632
(1.00) 		0.39
(1.00)
Del Peak 53(Xq22 3) 0 (0%) 263 0.731
(1.00) 		0.738
(1.00) 		0.375
(1.00) 		0.268
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.0696
(1.00) 		0.245
(1.00) 		0.263
(1.00) 		0.225
(1.00) 		0.131
(1.00) 		0.971
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 345

  • Number of significantly arm-level cnvs = 84

  • Number of selected clinical features = 13

  • 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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