Correlation between copy number variation genes (focal) and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C12805K4
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Rectum Adenocarcinoma (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/C12805K4
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 62 arm-level results and 11 clinical features across 162 patients, 2 significant findings detected with Q value < 0.25.

  • Del Peak 6(3q26.31) cnv correlated to 'Time to Death'.

  • Del Peak 30(18q21.2) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 62 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-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 Fisher's exact test Fisher's exact test t-test
Del Peak 6(3q26 31) 0 (0%) 145 8.16e-05
(0.0556) 		0.705
(1.00) 		0.0036
(1.00) 		0.0303
(1.00) 		0.216
(1.00) 		0.573
(1.00) 		0.2
(1.00) 		0.00346
(1.00) 		0.121
(1.00) 		0.0387
(1.00) 		0.251
(1.00)
Del Peak 30(18q21 2) 0 (0%) 19 0.653
(1.00) 		0.443
(1.00) 		1
(1.00) 		1
(1.00) 		0.00589
(1.00) 		0.0568
(1.00) 		0.208
(1.00) 		0.0231
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.000153
(0.104)
Amp Peak 1(1q21 3) 0 (0%) 114 0.538
(1.00) 		0.951
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.441
(1.00) 		0.106
(1.00) 		0.835
(1.00) 		0.0639
(1.00) 		0.691
(1.00) 		0.227
(1.00)
Amp Peak 2(1q32 2) 0 (0%) 114 0.0492
(1.00) 		0.645
(1.00) 		1
(1.00) 		1
(1.00) 		0.0297
(1.00) 		0.264
(1.00) 		0.357
(1.00) 		0.604
(1.00) 		0.362
(1.00) 		0.64
(1.00) 		0.0174
(1.00)
Amp Peak 3(5q22 3) 0 (0%) 143 0.529
(1.00) 		0.383
(1.00) 		0.81
(1.00) 		0.37
(1.00) 		0.881
(1.00) 		0.772
(1.00) 		0.743
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.372
(1.00)
Amp Peak 4(6p21 1) 0 (0%) 110 0.178
(1.00) 		0.528
(1.00) 		0.4
(1.00) 		0.0626
(1.00) 		0.428
(1.00) 		0.00855
(1.00) 		0.00762
(1.00) 		0.0299
(1.00) 		0.0844
(1.00) 		0.0957
(1.00) 		0.0836
(1.00)
Amp Peak 5(8p11 23) 0 (0%) 110 0.0852
(1.00) 		0.264
(1.00) 		0.0635
(1.00) 		0.222
(1.00) 		0.216
(1.00) 		0.457
(1.00) 		0.305
(1.00) 		0.223
(1.00) 		1
(1.00) 		0.0229
(1.00) 		0.289
(1.00)
Amp Peak 6(8p11 21) 0 (0%) 93 0.478
(1.00) 		0.541
(1.00) 		0.637
(1.00) 		0.154
(1.00) 		0.408
(1.00) 		0.814
(1.00) 		0.191
(1.00) 		0.074
(1.00) 		0.241
(1.00) 		0.00288
(1.00) 		0.574
(1.00)
Amp Peak 7(8q24 21) 0 (0%) 55 0.693
(1.00) 		0.228
(1.00) 		0.868
(1.00) 		0.0326
(1.00) 		0.49
(1.00) 		0.671
(1.00) 		0.533
(1.00) 		0.284
(1.00) 		0.665
(1.00) 		0.372
(1.00) 		0.763
(1.00)
Amp Peak 8(10q22 2) 0 (0%) 151 0.306
(1.00) 		0.686
(1.00) 		0.551
(1.00) 		0.592
(1.00) 		0.935
(1.00) 		0.914
(1.00) 		0.743
(1.00) 		0.969
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.939
(1.00)
Amp Peak 9(11p15 5) 0 (0%) 119 0.607
(1.00) 		0.969
(1.00) 		1
(1.00) 		0.188
(1.00) 		0.907
(1.00) 		0.195
(1.00) 		0.803
(1.00) 		0.258
(1.00) 		0.656
(1.00) 		0.938
(1.00) 		0.685
(1.00)
Amp Peak 10(11q13 3) 0 (0%) 136 0.456
(1.00) 		0.0577
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.494
(1.00) 		0.361
(1.00) 		0.288
(1.00) 		0.104
(1.00) 		0.591
(1.00) 		0.66
(1.00) 		0.0272
(1.00)
Amp Peak 11(12p13 33) 0 (0%) 121 0.984
(1.00) 		0.246
(1.00) 		0.589
(1.00) 		0.308
(1.00) 		0.418
(1.00) 		0.546
(1.00) 		0.105
(1.00) 		0.633
(1.00) 		0.171
(1.00) 		0.274
(1.00) 		0.339
(1.00)
Amp Peak 12(12p12 1) 0 (0%) 122 0.702
(1.00) 		0.334
(1.00) 		0.716
(1.00) 		0.191
(1.00) 		0.373
(1.00) 		0.516
(1.00) 		0.0872
(1.00) 		0.446
(1.00) 		0.161
(1.00) 		0.219
(1.00) 		0.102
(1.00)
Amp Peak 13(13q12 13) 0 (0%) 41 0.0417
(1.00) 		0.113
(1.00) 		0.718
(1.00) 		0.00387
(1.00) 		0.068
(1.00) 		0.0187
(1.00) 		0.254
(1.00) 		0.258
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.524
(1.00)
Amp Peak 14(13q12 2) 0 (0%) 42 0.052
(1.00) 		0.0514
(1.00) 		0.369
(1.00) 		0.00467
(1.00) 		0.0663
(1.00) 		0.027
(1.00) 		0.306
(1.00) 		0.307
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.524
(1.00)
Amp Peak 15(13q22 1) 0 (0%) 45 0.202
(1.00) 		0.337
(1.00) 		0.482
(1.00) 		0.00132
(0.894) 		0.202
(1.00) 		0.139
(1.00) 		0.289
(1.00) 		0.433
(1.00) 		0.67
(1.00) 		0.801
(1.00) 		0.861
(1.00)
Amp Peak 16(15q26 1) 0 (0%) 147 0.854
(1.00) 		0.944
(1.00) 		0.106
(1.00) 		0.362
(1.00) 		0.221
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.572
(1.00) 		0.0967
(1.00) 		0.375
(1.00) 		0.487
(1.00)
Amp Peak 17(16p11 2) 0 (0%) 117 0.183
(1.00) 		0.323
(1.00) 		0.862
(1.00) 		0.0205
(1.00) 		0.607
(1.00) 		0.146
(1.00) 		0.0837
(1.00) 		0.371
(1.00) 		0.67
(1.00) 		0.0597
(1.00) 		0.907
(1.00)
Amp Peak 18(17q12) 0 (0%) 119 0.653
(1.00) 		0.676
(1.00) 		0.215
(1.00) 		0.517
(1.00) 		0.725
(1.00) 		0.364
(1.00) 		0.335
(1.00) 		0.429
(1.00) 		0.343
(1.00) 		0.173
(1.00) 		0.31
(1.00)
Amp Peak 19(17q24 1) 0 (0%) 125 0.659
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.0401
(1.00) 		0.258
(1.00) 		0.266
(1.00) 		0.192
(1.00) 		0.204
(1.00) 		0.338
(1.00) 		0.221
(1.00) 		0.206
(1.00)
Amp Peak 20(19p13 2) 0 (0%) 130 0.0245
(1.00) 		0.451
(1.00) 		0.693
(1.00) 		0.0717
(1.00) 		0.228
(1.00) 		0.545
(1.00) 		0.578
(1.00) 		0.709
(1.00) 		0.599
(1.00) 		0.511
(1.00) 		0.554
(1.00)
Amp Peak 21(20q11 21) 0 (0%) 19 0.209
(1.00) 		0.099
(1.00) 		1
(1.00) 		0.000738
(0.499) 		0.55
(1.00) 		0.0956
(1.00) 		0.547
(1.00) 		0.0969
(1.00) 		0.533
(1.00) 		0.581
(1.00) 		0.486
(1.00)
Amp Peak 22(20q11 23) 0 (0%) 18 0.211
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.000498
(0.338) 		0.603
(1.00) 		0.0293
(1.00) 		0.433
(1.00) 		0.0857
(1.00) 		0.513
(1.00) 		0.581
(1.00) 		0.486
(1.00)
Amp Peak 23(20q13 31) 0 (0%) 17 0.217
(1.00) 		0.239
(1.00) 		0.8
(1.00) 		0.000498
(0.338) 		0.614
(1.00) 		0.0489
(1.00) 		0.493
(1.00) 		0.139
(1.00) 		0.492
(1.00) 		0.55
(1.00) 		0.446
(1.00)
Amp Peak 24(Xp22 2) 0 (0%) 129 0.945
(1.00) 		0.427
(1.00) 		0.0771
(1.00) 		0.303
(1.00) 		0.699
(1.00) 		0.654
(1.00) 		0.465
(1.00) 		0.598
(1.00) 		0.348
(1.00) 		0.273
(1.00) 		0.43
(1.00)
Amp Peak 25(Xq27 3) 0 (0%) 124 0.459
(1.00) 		0.225
(1.00) 		0.356
(1.00) 		0.3
(1.00) 		0.35
(1.00) 		0.743
(1.00) 		0.667
(1.00) 		0.645
(1.00) 		0.337
(1.00) 		0.685
(1.00) 		0.806
(1.00)
Del Peak 1(1p36 11) 0 (0%) 91 0.939
(1.00) 		0.617
(1.00) 		0.751
(1.00) 		0.56
(1.00) 		0.102
(1.00) 		0.215
(1.00) 		0.393
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.327
(1.00) 		0.0468
(1.00)
Del Peak 2(1p33) 0 (0%) 113 0.522
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.528
(1.00) 		0.229
(1.00) 		0.76
(1.00) 		0.637
(1.00) 		0.368
(1.00) 		0.547
(1.00) 		0.649
(1.00)
Del Peak 3(1p13 2) 0 (0%) 111 0.944
(1.00) 		0.646
(1.00) 		0.735
(1.00) 		0.347
(1.00) 		0.147
(1.00) 		0.779
(1.00) 		0.499
(1.00) 		0.182
(1.00) 		0.38
(1.00) 		0.688
(1.00) 		0.245
(1.00)
Del Peak 4(2p12) 0 (0%) 145 0.498
(1.00) 		0.175
(1.00) 		0.8
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.653
(1.00) 		0.285
(1.00) 		0.252
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.471
(1.00)
Del Peak 5(3p14 2) 0 (0%) 133 0.052
(1.00) 		0.811
(1.00) 		0.013
(1.00) 		0.456
(1.00) 		0.196
(1.00) 		0.943
(1.00) 		0.285
(1.00) 		0.0402
(1.00) 		0.292
(1.00) 		0.0853
(1.00) 		0.367
(1.00)
Del Peak 7(4p13) 0 (0%) 104 0.215
(1.00) 		0.877
(1.00) 		0.0996
(1.00) 		0.38
(1.00) 		0.748
(1.00) 		0.327
(1.00) 		0.961
(1.00) 		0.673
(1.00) 		0.00177
(1.00) 		0.399
(1.00) 		0.675
(1.00)
Del Peak 8(4q22 1) 0 (0%) 90 0.107
(1.00) 		0.378
(1.00) 		0.153
(1.00) 		0.393
(1.00) 		0.287
(1.00) 		0.714
(1.00) 		0.857
(1.00) 		0.622
(1.00) 		0.0892
(1.00) 		0.215
(1.00) 		0.078
(1.00)
Del Peak 9(4q35 1) 0 (0%) 90 0.294
(1.00) 		0.645
(1.00) 		0.428
(1.00) 		0.15
(1.00) 		0.445
(1.00) 		0.56
(1.00) 		0.957
(1.00) 		0.791
(1.00) 		0.0892
(1.00) 		0.118
(1.00) 		0.306
(1.00)
Del Peak 10(5q11 2) 0 (0%) 113 0.708
(1.00) 		0.836
(1.00) 		0.233
(1.00) 		0.347
(1.00) 		0.927
(1.00) 		0.871
(1.00) 		0.336
(1.00) 		0.253
(1.00) 		0.01
(1.00) 		0.888
(1.00) 		0.708
(1.00)
Del Peak 11(5q22 2) 0 (0%) 107 0.58
(1.00) 		0.56
(1.00) 		0.405
(1.00) 		0.222
(1.00) 		0.495
(1.00) 		0.423
(1.00) 		0.903
(1.00) 		0.565
(1.00) 		0.0176
(1.00) 		1
(1.00) 		0.374
(1.00)
Del Peak 12(6p25 3) 0 (0%) 138 0.409
(1.00) 		0.391
(1.00) 		0.825
(1.00) 		0.386
(1.00) 		0.213
(1.00) 		0.38
(1.00) 		0.67
(1.00) 		0.08
(1.00) 		0.217
(1.00) 		0.66
(1.00) 		0.979
(1.00)
Del Peak 13(6q26) 0 (0%) 132 0.4
(1.00) 		0.852
(1.00) 		0.158
(1.00) 		0.0138
(1.00) 		0.392
(1.00) 		0.0813
(1.00) 		0.677
(1.00) 		0.533
(1.00) 		0.308
(1.00) 		0.588
(1.00) 		0.217
(1.00)
Del Peak 14(7q31 1) 0 (0%) 158 0.174
(1.00) 		1
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.919
(1.00) 		1
(1.00) 		1
(1.00) 		0.548
(1.00)
Del Peak 15(8p23 2) 0 (0%) 62 0.71
(1.00) 		0.494
(1.00) 		0.872
(1.00) 		0.564
(1.00) 		0.201
(1.00) 		0.537
(1.00) 		0.799
(1.00) 		0.79
(1.00) 		0.0831
(1.00) 		0.386
(1.00) 		0.112
(1.00)
Del Peak 16(8p11 21) 0 (0%) 138 0.847
(1.00) 		0.184
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.812
(1.00) 		0.0829
(1.00) 		0.328
(1.00) 		0.217
(1.00) 		0.742
(1.00) 		0.123
(1.00)
Del Peak 17(10q21 1) 0 (0%) 125 0.498
(1.00) 		0.261
(1.00) 		0.574
(1.00) 		0.179
(1.00) 		0.828
(1.00) 		0.568
(1.00) 		0.107
(1.00) 		0.197
(1.00) 		0.0249
(1.00) 		0.109
(1.00) 		0.806
(1.00)
Del Peak 18(10q25 2) 0 (0%) 115 0.422
(1.00) 		0.369
(1.00) 		0.864
(1.00) 		0.0535
(1.00) 		0.148
(1.00) 		0.904
(1.00) 		0.563
(1.00) 		0.298
(1.00) 		0.00819
(1.00) 		0.204
(1.00) 		0.914
(1.00)
Del Peak 19(11q22 3) 0 (0%) 125 0.298
(1.00) 		0.453
(1.00) 		0.71
(1.00) 		0.0322
(1.00) 		0.635
(1.00) 		0.941
(1.00) 		0.0617
(1.00) 		0.272
(1.00) 		0.133
(1.00) 		0.164
(1.00) 		0.225
(1.00)
Del Peak 20(12p13 1) 0 (0%) 129 0.0863
(1.00) 		0.894
(1.00) 		0.845
(1.00) 		0.465
(1.00) 		0.891
(1.00) 		0.136
(1.00) 		0.28
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.568
(1.00) 		0.488
(1.00)
Del Peak 21(12q21 33) 0 (0%) 134 0.626
(1.00) 		0.292
(1.00) 		1
(1.00) 		0.469
(1.00) 		0.697
(1.00) 		0.851
(1.00) 		0.677
(1.00) 		0.254
(1.00) 		0.277
(1.00) 		0.314
(1.00) 		0.707
(1.00)
Del Peak 22(14q11 2) 0 (0%) 95 0.23
(1.00) 		0.427
(1.00) 		0.427
(1.00) 		0.0746
(1.00) 		0.617
(1.00) 		0.291
(1.00) 		0.724
(1.00) 		0.334
(1.00) 		0.232
(1.00) 		0.101
(1.00) 		0.501
(1.00)
Del Peak 23(14q31 1) 0 (0%) 93 0.607
(1.00) 		0.84
(1.00) 		0.27
(1.00) 		0.00787
(1.00) 		0.16
(1.00) 		0.0566
(1.00) 		0.606
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.436
(1.00) 		0.518
(1.00)
Del Peak 24(15q22 33) 0 (0%) 87 0.558
(1.00) 		0.86
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.0115
(1.00) 		0.262
(1.00) 		0.741
(1.00) 		0.0732
(1.00) 		0.0966
(1.00) 		0.575
(1.00) 		0.0338
(1.00)
Del Peak 25(16p13 3) 0 (0%) 149 0.00338
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.788
(1.00) 		0.181
(1.00) 		0.797
(1.00) 		0.135
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00)
Del Peak 26(16q23 1) 0 (0%) 139 0.925
(1.00) 		0.585
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.0144
(1.00) 		0.841
(1.00) 		0.327
(1.00) 		1
(1.00) 		1
(1.00) 		0.072
(1.00)
Del Peak 27(17p12) 0 (0%) 52 0.4
(1.00) 		0.0943
(1.00) 		0.866
(1.00) 		0.122
(1.00) 		0.0153
(1.00) 		0.893
(1.00) 		0.88
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.854
(1.00) 		0.73
(1.00)
Del Peak 28(17p11 2) 0 (0%) 60 0.775
(1.00) 		0.201
(1.00) 		0.514
(1.00) 		0.0783
(1.00) 		0.0832
(1.00) 		0.693
(1.00) 		0.357
(1.00) 		0.598
(1.00) 		0.671
(1.00) 		0.862
(1.00) 		0.689
(1.00)
Del Peak 29(17q25 3) 0 (0%) 138 0.103
(1.00) 		0.696
(1.00) 		0.119
(1.00) 		1
(1.00) 		0.366
(1.00) 		0.828
(1.00) 		0.13
(1.00) 		0.369
(1.00) 		0.217
(1.00) 		0.102
(1.00) 		0.627
(1.00)
Del Peak 31(18q22 1) 0 (0%) 24 0.653
(1.00) 		0.227
(1.00) 		0.825
(1.00) 		0.397
(1.00) 		0.0492
(1.00) 		0.337
(1.00) 		0.567
(1.00) 		0.126
(1.00) 		0.593
(1.00) 		0.585
(1.00) 		0.00206
(1.00)
Del Peak 32(19p13 3) 0 (0%) 124 0.816
(1.00) 		0.795
(1.00) 		1
(1.00) 		0.734
(1.00) 		0.297
(1.00) 		0.562
(1.00) 		0.251
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.693
(1.00)
Del Peak 33(20p12 1) 0 (0%) 102 0.131
(1.00) 		0.23
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.88
(1.00) 		0.473
(1.00) 		0.839
(1.00) 		0.0855
(1.00) 		0.466
(1.00) 		0.557
(1.00)
Del Peak 34(20p12 1) 0 (0%) 102 0.131
(1.00) 		0.23
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.88
(1.00) 		0.473
(1.00) 		0.839
(1.00) 		0.0855
(1.00) 		0.466
(1.00) 		0.557
(1.00)
Del Peak 35(21q11 2) 0 (0%) 92 0.996
(1.00) 		0.454
(1.00) 		0.633
(1.00) 		0.24
(1.00) 		0.139
(1.00) 		0.322
(1.00) 		0.764
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.295
(1.00)
Del Peak 36(22q13 31) 0 (0%) 96 0.0572
(1.00) 		0.255
(1.00) 		0.339
(1.00) 		0.563
(1.00) 		0.28
(1.00) 		0.00822
(1.00) 		0.207
(1.00) 		0.331
(1.00) 		0.688
(1.00) 		0.246
(1.00) 		0.425
(1.00)
Del Peak 37(Xp22 33) 0 (0%) 129 0.626
(1.00) 		0.681
(1.00) 		0.845
(1.00) 		0.716
(1.00) 		0.699
(1.00) 		0.856
(1.00) 		0.596
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.787
(1.00)
'Del Peak 6(3q26.31)' versus 'Time to Death'

P value = 8.16e-05 (logrank test), Q value = 0.056

Table S1.  Gene #31: 'Del Peak 6(3q26.31)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 125 11 0.2 - 121.1 (6.3)
DEL PEAK 6(3Q26.31) CNV 15 3 0.2 - 38.9 (2.8)
DEL PEAK 6(3Q26.31) WILD-TYPE 110 8 0.4 - 121.1 (7.0)

Figure S1.  Get High-res Image Gene #31: 'Del Peak 6(3q26.31)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 30(18q21.2)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000153 (t-test), Q value = 0.1

Table S2.  Gene #55: 'Del Peak 30(18q21.2)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 149 2.7 (5.4)
DEL PEAK 30(18Q21.2) CNV 130 2.9 (5.7)
DEL PEAK 30(18Q21.2) WILD-TYPE 19 0.6 (1.4)

Figure S2.  Get High-res Image Gene #55: 'Del Peak 30(18q21.2)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

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

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 62

  • Number of selected clinical features = 11

  • 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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