Correlation between copy number variation genes (focal events) and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C19K48K5
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 events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C19K48K5
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 75 focal events and 11 clinical features across 305 patients, no significant finding detected with Q value < 0.25.

  • No focal 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 75 focal events and 11 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 NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test t-test
AMP PEAK 1(1P36 22) MUTATION ANALYSIS 36 (12%) 269 0.534
(1.00) 		0.968
(1.00) 		0.247
(1.00) 		0.64
(1.00) 		0.427
(1.00) 		0.509
(1.00) 		0.0713
(1.00) 		0.944
(1.00) 		0.589
(1.00) 		0.561
(1.00) 		0.649
(1.00)
AMP PEAK 2(1Q21 3) MUTATION ANALYSIS 108 (35%) 197 0.379
(1.00) 		0.576
(1.00) 		0.711
(1.00) 		0.215
(1.00) 		0.228
(1.00) 		0.0638
(1.00) 		0.391
(1.00) 		0.118
(1.00) 		0.00891
(1.00) 		0.368
(1.00) 		0.24
(1.00)
AMP PEAK 3(1Q42 3) MUTATION ANALYSIS 105 (34%) 200 0.846
(1.00) 		0.935
(1.00) 		0.955
(1.00) 		0.436
(1.00) 		0.511
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.00575
(1.00) 		0.238
(1.00) 		0.92
(1.00) 		0.53
(1.00)
AMP PEAK 4(3Q26 2) MUTATION ANALYSIS 101 (33%) 204 0.836
(1.00) 		0.569
(1.00) 		0.875
(1.00) 		0.243
(1.00) 		0.357
(1.00) 		0.0446
(1.00) 		0.535
(1.00) 		0.961
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.14
(1.00)
AMP PEAK 5(5P13 1) MUTATION ANALYSIS 87 (29%) 218 0.308
(1.00) 		0.0774
(1.00) 		0.507
(1.00) 		0.307
(1.00) 		0.416
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.411
(1.00) 		0.603
(1.00) 		0.575
(1.00)
AMP PEAK 6(6P21 1) MUTATION ANALYSIS 80 (26%) 225 0.409
(1.00) 		0.0194
(1.00) 		0.247
(1.00) 		0.058
(1.00) 		0.658
(1.00) 		0.086
(1.00) 		1
(1.00) 		0.0181
(1.00) 		0.0801
(1.00) 		0.0721
(1.00) 		0.63
(1.00)
AMP PEAK 7(6Q12) MUTATION ANALYSIS 60 (20%) 245 0.0985
(1.00) 		0.899
(1.00) 		0.549
(1.00) 		0.31
(1.00) 		0.531
(1.00) 		0.685
(1.00) 		0.463
(1.00) 		0.0974
(1.00) 		0.14
(1.00) 		0.127
(1.00) 		0.158
(1.00)
AMP PEAK 8(6Q21) MUTATION ANALYSIS 56 (18%) 249 0.505
(1.00) 		0.915
(1.00) 		0.32
(1.00) 		0.705
(1.00) 		0.321
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.119
(1.00) 		0.315
(1.00) 		0.369
(1.00)
AMP PEAK 9(7P22 3) MUTATION ANALYSIS 157 (51%) 148 0.583
(1.00) 		0.0286
(1.00) 		0.642
(1.00) 		0.887
(1.00) 		0.337
(1.00) 		0.371
(1.00) 		0.101
(1.00) 		0.361
(1.00) 		0.716
(1.00) 		0.909
(1.00) 		0.336
(1.00)
AMP PEAK 10(7P11 2) MUTATION ANALYSIS 143 (47%) 162 0.404
(1.00) 		0.0603
(1.00) 		0.563
(1.00) 		0.552
(1.00) 		0.794
(1.00) 		0.235
(1.00) 		0.29
(1.00) 		0.674
(1.00) 		0.454
(1.00) 		0.806
(1.00) 		0.185
(1.00)
AMP PEAK 11(7Q21 2) MUTATION ANALYSIS 137 (45%) 168 0.199
(1.00) 		0.292
(1.00) 		0.886
(1.00) 		0.867
(1.00) 		0.424
(1.00) 		0.143
(1.00) 		0.157
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.0272
(1.00)
AMP PEAK 12(8P23 1) MUTATION ANALYSIS 121 (40%) 184 0.472
(1.00) 		0.172
(1.00) 		0.596
(1.00) 		0.21
(1.00) 		0.756
(1.00) 		0.492
(1.00) 		0.119
(1.00) 		0.906
(1.00) 		0.118
(1.00) 		0.291
(1.00) 		0.817
(1.00)
AMP PEAK 13(8Q24 21) MUTATION ANALYSIS 204 (67%) 101 0.504
(1.00) 		0.0168
(1.00) 		0.61
(1.00) 		0.0851
(1.00) 		0.401
(1.00) 		0.559
(1.00) 		0.71
(1.00) 		0.0865
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.21
(1.00)
AMP PEAK 14(9P24 1) MUTATION ANALYSIS 49 (16%) 256 0.98
(1.00) 		0.65
(1.00) 		0.228
(1.00) 		0.202
(1.00) 		0.0896
(1.00) 		1
(1.00) 		1
(1.00) 		0.436
(1.00) 		0.0852
(1.00) 		0.935
(1.00) 		0.75
(1.00)
AMP PEAK 15(9Q34 3) MUTATION ANALYSIS 74 (24%) 231 0.202
(1.00) 		0.0461
(1.00) 		0.227
(1.00) 		0.18
(1.00) 		0.452
(1.00) 		0.948
(1.00) 		0.494
(1.00) 		0.00896
(1.00) 		0.366
(1.00) 		0.832
(1.00) 		0.0338
(1.00)
AMP PEAK 16(10Q22 2) MUTATION ANALYSIS 56 (18%) 249 0.501
(1.00) 		0.643
(1.00) 		0.123
(1.00) 		0.673
(1.00) 		0.526
(1.00) 		0.877
(1.00) 		0.88
(1.00) 		0.868
(1.00) 		0.616
(1.00) 		0.39
(1.00) 		0.419
(1.00)
AMP PEAK 17(10Q26 13) MUTATION ANALYSIS 61 (20%) 244 0.722
(1.00) 		0.674
(1.00) 		0.207
(1.00) 		0.519
(1.00) 		0.749
(1.00) 		0.647
(1.00) 		0.77
(1.00) 		0.546
(1.00) 		0.63
(1.00) 		0.855
(1.00) 		0.578
(1.00)
AMP PEAK 18(11P13) MUTATION ANALYSIS 54 (18%) 251 0.941
(1.00) 		0.687
(1.00) 		0.321
(1.00) 		0.0659
(1.00) 		0.409
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.36
(1.00) 		0.868
(1.00) 		0.235
(1.00)
AMP PEAK 19(11Q13 3) MUTATION ANALYSIS 68 (22%) 237 0.288
(1.00) 		0.518
(1.00) 		0.785
(1.00) 		0.432
(1.00) 		0.114
(1.00) 		0.359
(1.00) 		1
(1.00) 		0.64
(1.00) 		0.655
(1.00) 		0.967
(1.00) 		0.556
(1.00)
AMP PEAK 20(12P12 1) MUTATION ANALYSIS 86 (28%) 219 0.469
(1.00) 		0.19
(1.00) 		0.373
(1.00) 		0.0199
(1.00) 		0.144
(1.00) 		0.953
(1.00) 		1
(1.00) 		0.177
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.927
(1.00)
AMP PEAK 21(12Q15) MUTATION ANALYSIS 77 (25%) 228 0.661
(1.00) 		0.449
(1.00) 		0.45
(1.00) 		0.107
(1.00) 		0.179
(1.00) 		0.812
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.374
(1.00) 		0.535
(1.00) 		0.264
(1.00)
AMP PEAK 22(13Q12 3) MUTATION ANALYSIS 116 (38%) 189 0.0482
(1.00) 		0.324
(1.00) 		0.64
(1.00) 		0.475
(1.00) 		0.511
(1.00) 		0.781
(1.00) 		0.717
(1.00) 		0.663
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.399
(1.00)
AMP PEAK 23(13Q22 1) MUTATION ANALYSIS 121 (40%) 184 0.526
(1.00) 		0.48
(1.00) 		0.671
(1.00) 		0.6
(1.00) 		0.812
(1.00) 		0.492
(1.00) 		0.338
(1.00) 		0.212
(1.00) 		0.707
(1.00) 		0.575
(1.00) 		0.373
(1.00)
AMP PEAK 24(15Q26 1) MUTATION ANALYSIS 69 (23%) 236 0.744
(1.00) 		0.616
(1.00) 		0.566
(1.00) 		0.484
(1.00) 		0.109
(1.00) 		0.147
(1.00) 		0.122
(1.00) 		0.239
(1.00) 		0.658
(1.00) 		0.371
(1.00) 		0.887
(1.00)
AMP PEAK 25(17Q12) MUTATION ANALYSIS 92 (30%) 213 0.747
(1.00) 		0.202
(1.00) 		0.886
(1.00) 		0.912
(1.00) 		0.913
(1.00) 		0.00297
(1.00) 		0.0962
(1.00) 		0.0102
(1.00) 		0.435
(1.00) 		0.00116
(0.953) 		0.149
(1.00)
AMP PEAK 26(18Q11 2) MUTATION ANALYSIS 90 (30%) 215 0.0985
(1.00) 		0.0923
(1.00) 		0.64
(1.00) 		0.508
(1.00) 		0.433
(1.00) 		0.651
(1.00) 		0.609
(1.00) 		0.0961
(1.00) 		0.0254
(1.00) 		0.0499
(1.00) 		0.117
(1.00)
AMP PEAK 27(19Q12) MUTATION ANALYSIS 90 (30%) 215 0.0138
(1.00) 		0.0862
(1.00) 		0.817
(1.00) 		0.00671
(1.00) 		0.903
(1.00) 		0.107
(1.00) 		0.898
(1.00) 		0.259
(1.00) 		0.0254
(1.00) 		0.278
(1.00) 		0.269
(1.00)
AMP PEAK 28(20Q13 2) MUTATION ANALYSIS 201 (66%) 104 0.613
(1.00) 		0.143
(1.00) 		0.446
(1.00) 		0.179
(1.00) 		0.172
(1.00) 		0.251
(1.00) 		0.0256
(1.00) 		0.0222
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.193
(1.00)
AMP PEAK 29(XQ27 3) MUTATION ANALYSIS 60 (20%) 245 0.838
(1.00) 		0.0382
(1.00) 		0.0233
(1.00) 		0.348
(1.00) 		0.325
(1.00) 		1
(1.00) 		1
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.769
(1.00) 		0.389
(1.00)
DEL PEAK 1(1P36 11) MUTATION ANALYSIS 83 (27%) 222 0.817
(1.00) 		0.65
(1.00) 		0.101
(1.00) 		0.104
(1.00) 		0.877
(1.00) 		0.496
(1.00) 		0.187
(1.00) 		0.0283
(1.00) 		0.0903
(1.00) 		0.0393
(1.00) 		0.286
(1.00)
DEL PEAK 2(1P13 2) MUTATION ANALYSIS 59 (19%) 246 0.164
(1.00) 		0.972
(1.00) 		0.71
(1.00) 		0.398
(1.00) 		0.537
(1.00) 		0.726
(1.00) 		0.656
(1.00) 		0.36
(1.00) 		0.624
(1.00) 		0.484
(1.00) 		0.482
(1.00)
DEL PEAK 3(1Q44) MUTATION ANALYSIS 23 (8%) 282 0.00467
(1.00) 		0.0435
(1.00) 		0.665
(1.00) 		0.494
(1.00) 		0.745
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.908
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.0732
(1.00)
DEL PEAK 4(2Q32 1) MUTATION ANALYSIS 42 (14%) 263 0.327
(1.00) 		0.68
(1.00) 		0.392
(1.00) 		0.127
(1.00) 		0.297
(1.00) 		1
(1.00) 		0.734
(1.00) 		0.0932
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.105
(1.00)
DEL PEAK 5(2Q37 2) MUTATION ANALYSIS 47 (15%) 258 0.547
(1.00) 		0.777
(1.00) 		0.583
(1.00) 		0.945
(1.00) 		0.865
(1.00) 		0.926
(1.00) 		0.0746
(1.00) 		0.411
(1.00) 		1
(1.00) 		0.0265
(1.00) 		0.522
(1.00)
DEL PEAK 6(3P26 2) MUTATION ANALYSIS 83 (27%) 222 0.881
(1.00) 		0.267
(1.00) 		0.452
(1.00) 		0.588
(1.00) 		0.175
(1.00) 		0.254
(1.00) 		0.598
(1.00) 		0.609
(1.00) 		0.395
(1.00) 		0.557
(1.00) 		0.616
(1.00)
DEL PEAK 7(3P14 2) MUTATION ANALYSIS 102 (33%) 203 0.299
(1.00) 		0.618
(1.00) 		0.465
(1.00) 		0.977
(1.00) 		0.327
(1.00) 		0.537
(1.00) 		0.62
(1.00) 		0.0467
(1.00) 		0.69
(1.00) 		0.0268
(1.00) 		0.596
(1.00)
DEL PEAK 8(3Q26 31) MUTATION ANALYSIS 34 (11%) 271 0.428
(1.00) 		0.797
(1.00) 		0.558
(1.00) 		0.213
(1.00) 		0.296
(1.00) 		0.111
(1.00) 		0.711
(1.00) 		0.312
(1.00) 		0.567
(1.00) 		0.751
(1.00) 		0.0982
(1.00)
DEL PEAK 9(4P16 3) MUTATION ANALYSIS 112 (37%) 193 0.376
(1.00) 		0.422
(1.00) 		0.397
(1.00) 		0.0168
(1.00) 		0.648
(1.00) 		0.0956
(1.00) 		0.903
(1.00) 		0.251
(1.00) 		0.71
(1.00) 		0.154
(1.00) 		0.265
(1.00)
DEL PEAK 10(4Q22 1) MUTATION ANALYSIS 135 (44%) 170 0.364
(1.00) 		0.185
(1.00) 		0.646
(1.00) 		0.286
(1.00) 		0.587
(1.00) 		0.67
(1.00) 		0.813
(1.00) 		0.229
(1.00) 		0.248
(1.00) 		0.29
(1.00) 		0.131
(1.00)
DEL PEAK 11(4Q34 3) MUTATION ANALYSIS 127 (42%) 178 0.502
(1.00) 		0.134
(1.00) 		0.236
(1.00) 		0.175
(1.00) 		0.988
(1.00) 		0.463
(1.00) 		0.475
(1.00) 		0.169
(1.00) 		0.132
(1.00) 		0.128
(1.00) 		0.356
(1.00)
DEL PEAK 12(5Q11 2) MUTATION ANALYSIS 103 (34%) 202 0.836
(1.00) 		0.0599
(1.00) 		0.0653
(1.00) 		0.212
(1.00) 		0.466
(1.00) 		0.449
(1.00) 		0.621
(1.00) 		0.00782
(1.00) 		0.231
(1.00) 		0.102
(1.00) 		0.363
(1.00)
DEL PEAK 13(5Q23 2) MUTATION ANALYSIS 93 (30%) 212 0.36
(1.00) 		0.403
(1.00) 		0.0146
(1.00) 		0.559
(1.00) 		0.407
(1.00) 		0.106
(1.00) 		0.611
(1.00) 		0.0181
(1.00) 		0.439
(1.00) 		0.102
(1.00) 		0.898
(1.00)
DEL PEAK 14(6P25 3) MUTATION ANALYSIS 68 (22%) 237 0.206
(1.00) 		0.296
(1.00) 		0.91
(1.00) 		0.682
(1.00) 		0.801
(1.00) 		0.0822
(1.00) 		0.485
(1.00) 		0.355
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.61
(1.00)
DEL PEAK 15(6Q26) MUTATION ANALYSIS 62 (20%) 243 0.655
(1.00) 		0.12
(1.00) 		0.196
(1.00) 		0.148
(1.00) 		0.871
(1.00) 		0.161
(1.00) 		0.245
(1.00) 		0.344
(1.00) 		0.151
(1.00) 		0.0218
(1.00) 		0.272
(1.00)
DEL PEAK 16(7Q31 1) MUTATION ANALYSIS 44 (14%) 261 0.0281
(1.00) 		0.182
(1.00) 		0.6
(1.00) 		0.198
(1.00) 		0.0237
(1.00) 		0.52
(1.00) 		0.096
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.619
(1.00)
DEL PEAK 17(7Q36 3) MUTATION ANALYSIS 58 (19%) 247 0.291
(1.00) 		0.794
(1.00) 		0.216
(1.00) 		0.313
(1.00) 		0.027
(1.00) 		1
(1.00) 		0.458
(1.00) 		0.182
(1.00) 		0.129
(1.00) 		0.88
(1.00) 		0.111
(1.00)
DEL PEAK 18(8P23 2) MUTATION ANALYSIS 77 (25%) 228 0.831
(1.00) 		0.0273
(1.00) 		0.319
(1.00) 		0.62
(1.00) 		0.285
(1.00) 		0.506
(1.00) 		0.284
(1.00) 		0.212
(1.00) 		1
(1.00) 		0.158
(1.00) 		0.0495
(1.00)
DEL PEAK 19(9P23) MUTATION ANALYSIS 120 (39%) 185 0.0332
(1.00) 		0.206
(1.00) 		0.0171
(1.00) 		0.125
(1.00) 		0.37
(1.00) 		0.693
(1.00) 		1
(1.00) 		0.658
(1.00) 		0.439
(1.00) 		0.88
(1.00) 		0.223
(1.00)
DEL PEAK 20(9P21 3) MUTATION ANALYSIS 118 (39%) 187 0.261
(1.00) 		0.209
(1.00) 		0.455
(1.00) 		0.0618
(1.00) 		0.366
(1.00) 		0.434
(1.00) 		0.904
(1.00) 		0.102
(1.00) 		0.436
(1.00) 		0.533
(1.00) 		0.669
(1.00)
DEL PEAK 21(9Q21 11) MUTATION ANALYSIS 73 (24%) 232 0.624
(1.00) 		0.845
(1.00) 		0.139
(1.00) 		0.0248
(1.00) 		0.914
(1.00) 		0.106
(1.00) 		0.783
(1.00) 		0.324
(1.00) 		0.674
(1.00) 		0.749
(1.00) 		0.32
(1.00)
DEL PEAK 22(10P15 1) MUTATION ANALYSIS 38 (12%) 267 0.182
(1.00) 		0.23
(1.00) 		0.125
(1.00) 		0.502
(1.00) 		0.189
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.27
(1.00) 		1
(1.00) 		0.225
(1.00) 		0.444
(1.00)
DEL PEAK 23(10Q22 3) MUTATION ANALYSIS 49 (16%) 256 0.853
(1.00) 		0.00365
(1.00) 		0.373
(1.00) 		0.0038
(1.00) 		0.829
(1.00) 		0.597
(1.00) 		0.752
(1.00) 		0.357
(1.00) 		0.313
(1.00) 		0.806
(1.00) 		0.494
(1.00)
DEL PEAK 24(10Q23 31) MUTATION ANALYSIS 73 (24%) 232 0.387
(1.00) 		0.00235
(1.00) 		0.0585
(1.00) 		0.00675
(1.00) 		0.708
(1.00) 		0.613
(1.00) 		0.682
(1.00) 		0.181
(1.00) 		0.674
(1.00) 		0.904
(1.00) 		0.883
(1.00)
DEL PEAK 25(11P15 4) MUTATION ANALYSIS 59 (19%) 246 0.0577
(1.00) 		0.18
(1.00) 		0.413
(1.00) 		0.00304
(1.00) 		0.541
(1.00) 		0.941
(1.00) 		0.298
(1.00) 		0.00264
(1.00) 		0.135
(1.00) 		0.0217
(1.00) 		0.0995
(1.00)
DEL PEAK 26(11Q23 2) MUTATION ANALYSIS 62 (20%) 243 0.095
(1.00) 		0.169
(1.00) 		0.374
(1.00) 		0.298
(1.00) 		0.267
(1.00) 		0.00828
(1.00) 		0.562
(1.00) 		0.542
(1.00) 		0.633
(1.00) 		0.222
(1.00) 		0.479
(1.00)
DEL PEAK 27(12P13 31) MUTATION ANALYSIS 50 (16%) 255 0.788
(1.00) 		0.201
(1.00) 		0.167
(1.00) 		0.114
(1.00) 		0.571
(1.00) 		0.476
(1.00) 		1
(1.00) 		0.0288
(1.00) 		0.0896
(1.00) 		0.393
(1.00) 		0.994
(1.00)
DEL PEAK 28(13Q12 11) MUTATION ANALYSIS 44 (14%) 261 0.269
(1.00) 		0.186
(1.00) 		0.993
(1.00) 		0.583
(1.00) 		0.714
(1.00) 		0.619
(1.00) 		0.184
(1.00) 		0.741
(1.00) 		0.0096
(1.00) 		0.463
(1.00) 		0.125
(1.00)
DEL PEAK 29(14Q21 1) MUTATION ANALYSIS 71 (23%) 234 0.311
(1.00) 		0.464
(1.00) 		0.18
(1.00) 		0.0259
(1.00) 		0.561
(1.00) 		0.0283
(1.00) 		0.781
(1.00) 		0.747
(1.00) 		0.666
(1.00) 		0.955
(1.00) 		0.785
(1.00)
DEL PEAK 30(14Q32 33) MUTATION ANALYSIS 89 (29%) 216 0.669
(1.00) 		0.537
(1.00) 		0.105
(1.00) 		0.499
(1.00) 		0.31
(1.00) 		0.00804
(1.00) 		0.52
(1.00) 		0.786
(1.00) 		0.42
(1.00) 		0.0828
(1.00) 		0.776
(1.00)
DEL PEAK 31(15Q15 1) MUTATION ANALYSIS 79 (26%) 226 0.545
(1.00) 		0.172
(1.00) 		0.225
(1.00) 		0.0109
(1.00) 		0.716
(1.00) 		0.0296
(1.00) 		1
(1.00) 		0.011
(1.00) 		0.0141
(1.00) 		0.12
(1.00) 		0.17
(1.00)
DEL PEAK 32(16P13 3) MUTATION ANALYSIS 58 (19%) 247 0.568
(1.00) 		0.0133
(1.00) 		0.129
(1.00) 		0.0951
(1.00) 		0.244
(1.00) 		0.682
(1.00) 		0.299
(1.00) 		0.0117
(1.00) 		0.621
(1.00) 		0.159
(1.00) 		0.9
(1.00)
DEL PEAK 33(16Q23 1) MUTATION ANALYSIS 118 (39%) 187 0.265
(1.00) 		0.284
(1.00) 		0.014
(1.00) 		0.756
(1.00) 		0.58
(1.00) 		0.0665
(1.00) 		0.151
(1.00) 		0.103
(1.00) 		0.113
(1.00) 		0.123
(1.00) 		0.259
(1.00)
DEL PEAK 34(17P12) MUTATION ANALYSIS 115 (38%) 190 0.202
(1.00) 		0.422
(1.00) 		0.485
(1.00) 		0.0495
(1.00) 		0.86
(1.00) 		0.103
(1.00) 		0.545
(1.00) 		0.0199
(1.00) 		0.108
(1.00) 		0.116
(1.00) 		0.455
(1.00)
DEL PEAK 35(17Q24 3) MUTATION ANALYSIS 55 (18%) 250 0.494
(1.00) 		0.0766
(1.00) 		0.459
(1.00) 		0.502
(1.00) 		0.429
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.358
(1.00) 		0.595
(1.00) 		0.0548
(1.00)
DEL PEAK 36(18Q21 2) MUTATION ANALYSIS 133 (44%) 172 0.602
(1.00) 		0.94
(1.00) 		0.491
(1.00) 		0.00222
(1.00) 		0.308
(1.00) 		0.14
(1.00) 		0.906
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.129
(1.00) 		0.00215
(1.00)
DEL PEAK 37(19P13 3) MUTATION ANALYSIS 99 (32%) 206 0.88
(1.00) 		0.138
(1.00) 		0.365
(1.00) 		0.186
(1.00) 		0.787
(1.00) 		0.403
(1.00) 		0.262
(1.00) 		0.294
(1.00) 		0.00541
(1.00) 		0.835
(1.00) 		0.264
(1.00)
DEL PEAK 38(19Q13 11) MUTATION ANALYSIS 43 (14%) 262 0.121
(1.00) 		0.154
(1.00) 		0.716
(1.00) 		0.494
(1.00) 		0.543
(1.00) 		0.715
(1.00) 		0.867
(1.00) 		0.545
(1.00) 		0.258
(1.00) 		0.449
(1.00) 		0.372
(1.00)
DEL PEAK 39(20P12 1) MUTATION ANALYSIS 52 (17%) 253 0.561
(1.00) 		0.397
(1.00) 		0.112
(1.00) 		0.924
(1.00) 		0.684
(1.00) 		0.49
(1.00) 		0.756
(1.00) 		0.807
(1.00) 		0.341
(1.00) 		0.939
(1.00) 		0.123
(1.00)
DEL PEAK 40(20P12 1) MUTATION ANALYSIS 52 (17%) 253 0.561
(1.00) 		0.397
(1.00) 		0.112
(1.00) 		0.924
(1.00) 		0.684
(1.00) 		0.49
(1.00) 		0.756
(1.00) 		0.807
(1.00) 		0.341
(1.00) 		0.939
(1.00) 		0.123
(1.00)
DEL PEAK 41(21Q11 2) MUTATION ANALYSIS 107 (35%) 198 0.534
(1.00) 		0.00316
(1.00) 		0.123
(1.00) 		0.0419
(1.00) 		0.782
(1.00) 		0.676
(1.00) 		0.0139
(1.00) 		0.855
(1.00) 		0.246
(1.00) 		0.361
(1.00) 		0.399
(1.00)
DEL PEAK 42(21Q22 13) MUTATION ANALYSIS 114 (37%) 191 0.692
(1.00) 		0.0472
(1.00) 		0.535
(1.00) 		0.0644
(1.00) 		0.98
(1.00) 		0.395
(1.00) 		0.185
(1.00) 		0.763
(1.00) 		0.715
(1.00) 		0.687
(1.00) 		0.649
(1.00)
DEL PEAK 43(22Q13 31) MUTATION ANALYSIS 101 (33%) 204 0.402
(1.00) 		0.673
(1.00) 		0.53
(1.00) 		0.0358
(1.00) 		0.507
(1.00) 		0.584
(1.00) 		0.535
(1.00) 		0.221
(1.00) 		0.0422
(1.00) 		0.572
(1.00) 		0.0977
(1.00)
DEL PEAK 44(XP22 2) MUTATION ANALYSIS 61 (20%) 244 0.769
(1.00) 		0.528
(1.00) 		0.465
(1.00) 		0.472
(1.00) 		0.75
(1.00) 		0.419
(1.00) 		0.306
(1.00) 		0.573
(1.00) 		0.63
(1.00) 		0.431
(1.00) 		0.925
(1.00)
DEL PEAK 45(XP21 1) MUTATION ANALYSIS 52 (17%) 253 0.584
(1.00) 		0.851
(1.00) 		0.284
(1.00) 		0.486
(1.00) 		0.978
(1.00) 		0.613
(1.00) 		0.0608
(1.00) 		0.81
(1.00) 		0.341
(1.00) 		0.00426
(1.00) 		0.177
(1.00)
DEL PEAK 46(XQ21 33) MUTATION ANALYSIS 42 (14%) 263 0.271
(1.00) 		0.93
(1.00) 		0.257
(1.00) 		0.368
(1.00) 		0.584
(1.00) 		0.924
(1.00) 		0.307
(1.00) 		0.545
(1.00) 		1
(1.00) 		0.207
(1.00) 		0.82
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 305

  • Number of significantly focal cnvs = 75

  • 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

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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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