Correlation between copy number variation genes (focal events) and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1B856F4
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/C1B856F4
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 66 focal events and 10 clinical features across 152 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 66 focal events and 10 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 KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED 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 t-test t-test t-test
AMP PEAK 1(1P34 3) MUTATION ANALYSIS 46 (30%) 106 0.724
(1.00) 		0.0243
(1.00) 		0.352
(1.00) 		0.676
(1.00) 		0.249
(1.00) 		0.599
(1.00) 		0.41
(1.00) 		0.477
(1.00) 		0.11
(1.00) 		0.465
(1.00)
AMP PEAK 2(1Q21 3) MUTATION ANALYSIS 78 (51%) 74 0.159
(1.00) 		0.284
(1.00) 		0.0304
(1.00) 		0.524
(1.00) 		0.0025
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.174
(1.00) 		0.0295
(1.00) 		0.074
(1.00)
AMP PEAK 3(1Q23 3) MUTATION ANALYSIS 84 (55%) 68 0.746
(1.00) 		0.142
(1.00) 		0.116
(1.00) 		0.731
(1.00) 		0.0221
(1.00) 		0.00933
(1.00) 		0.565
(1.00) 		0.169
(1.00) 		0.161
(1.00) 		0.084
(1.00)
AMP PEAK 4(3P25 2) MUTATION ANALYSIS 73 (48%) 79 0.192
(1.00) 		0.18
(1.00) 		0.834
(1.00) 		0.236
(1.00) 		0.276
(1.00) 		0.683
(1.00) 		0.0561
(1.00) 		0.0113
(1.00) 		0.915
(1.00) 		0.436
(1.00)
AMP PEAK 5(3Q26 32) MUTATION ANALYSIS 84 (55%) 68 0.096
(1.00) 		0.642
(1.00) 		0.882
(1.00) 		0.617
(1.00) 		0.253
(1.00) 		0.867
(1.00) 		1
(1.00) 		0.2
(1.00) 		0.823
(1.00) 		0.906
(1.00)
AMP PEAK 6(4P16 3) MUTATION ANALYSIS 34 (22%) 118 0.106
(1.00) 		0.877
(1.00) 		0.0297
(1.00) 		0.0638
(1.00) 		0.0308
(1.00) 		0.0281
(1.00) 		0.0704
(1.00) 		0.399
(1.00) 		0.473
(1.00) 		0.862
(1.00)
AMP PEAK 7(4Q13 3) MUTATION ANALYSIS 25 (16%) 127 0.164
(1.00) 		0.0294
(1.00) 		0.817
(1.00) 		0.278
(1.00) 		0.846
(1.00) 		0.78
(1.00) 		0.127
(1.00) 		0.329
(1.00) 		0.89
(1.00) 		0.52
(1.00)
AMP PEAK 8(5P15 1) MUTATION ANALYSIS 72 (47%) 80 0.534
(1.00) 		0.736
(1.00) 		0.899
(1.00) 		0.491
(1.00) 		0.088
(1.00) 		0.145
(1.00) 		0.259
(1.00) 		0.294
(1.00) 		0.539
(1.00) 		0.0642
(1.00)
AMP PEAK 9(6P22 3) MUTATION ANALYSIS 63 (41%) 89 0.576
(1.00) 		0.529
(1.00) 		0.19
(1.00) 		0.0256
(1.00) 		0.185
(1.00) 		0.823
(1.00) 		0.702
(1.00) 		0.883
(1.00) 		0.59
(1.00) 		0.0199
(1.00)
AMP PEAK 10(6Q12) MUTATION ANALYSIS 26 (17%) 126 0.561
(1.00) 		0.135
(1.00) 		0.862
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.133
(1.00) 		0.181
(1.00) 		0.143
(1.00) 		0.0751
(1.00)
AMP PEAK 11(6Q21) MUTATION ANALYSIS 17 (11%) 135 0.65
(1.00) 		0.691
(1.00) 		0.659
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.468
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.302
(1.00) 		0.958
(1.00)
AMP PEAK 12(7P21 1) MUTATION ANALYSIS 74 (49%) 78 0.868
(1.00) 		0.189
(1.00) 		0.427
(1.00) 		0.638
(1.00) 		0.257
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.0959
(1.00) 		0.748
(1.00)
AMP PEAK 13(7P11 2) MUTATION ANALYSIS 77 (51%) 75 0.916
(1.00) 		0.019
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.03
(1.00) 		0.915
(1.00) 		0.85
(1.00) 		0.622
(1.00) 		0.248
(1.00) 		0.246
(1.00)
AMP PEAK 14(8P11 23) MUTATION ANALYSIS 49 (32%) 103 0.542
(1.00) 		0.856
(1.00) 		0.703
(1.00) 		0.881
(1.00) 		0.268
(1.00) 		0.604
(1.00) 		0.548
(1.00) 		0.559
(1.00) 		0.103
(1.00) 		0.75
(1.00)
AMP PEAK 15(8P11 21) MUTATION ANALYSIS 49 (32%) 103 0.264
(1.00) 		0.685
(1.00) 		0.631
(1.00) 		0.804
(1.00) 		0.654
(1.00) 		0.228
(1.00) 		0.158
(1.00) 		0.39
(1.00) 		0.0488
(1.00) 		0.625
(1.00)
AMP PEAK 16(8Q22 3) MUTATION ANALYSIS 98 (64%) 54 0.243
(1.00) 		0.506
(1.00) 		0.794
(1.00) 		0.648
(1.00) 		0.206
(1.00) 		0.776
(1.00) 		0.0468
(1.00) 		0.68
(1.00) 		0.242
(1.00) 		0.0732
(1.00)
AMP PEAK 17(8Q24 21) MUTATION ANALYSIS 94 (62%) 58 0.261
(1.00) 		0.78
(1.00) 		0.378
(1.00) 		0.698
(1.00) 		0.54
(1.00) 		0.401
(1.00) 		0.0496
(1.00) 		0.548
(1.00) 		0.75
(1.00) 		0.0847
(1.00)
AMP PEAK 18(10P15 1) MUTATION ANALYSIS 62 (41%) 90 0.349
(1.00) 		0.0204
(1.00) 		0.689
(1.00) 		0.792
(1.00) 		0.11
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.46
(1.00) 		0.626
(1.00)
AMP PEAK 19(11Q13 3) MUTATION ANALYSIS 59 (39%) 93 0.394
(1.00) 		0.0602
(1.00) 		0.514
(1.00) 		0.661
(1.00) 		0.206
(1.00) 		0.0875
(1.00) 		0.44
(1.00) 		0.429
(1.00) 		0.256
(1.00) 		0.43
(1.00)
AMP PEAK 20(11Q22 1) MUTATION ANALYSIS 26 (17%) 126 0.169
(1.00) 		0.204
(1.00) 		0.975
(1.00) 		0.619
(1.00) 		0.726
(1.00) 		0.727
(1.00) 		0.623
(1.00) 		0.69
(1.00) 		0.327
(1.00) 		0.952
(1.00)
AMP PEAK 21(12Q15) MUTATION ANALYSIS 48 (32%) 104 0.702
(1.00) 		0.545
(1.00) 		0.536
(1.00) 		0.27
(1.00) 		0.243
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.14
(1.00) 		0.464
(1.00)
AMP PEAK 22(13Q22 1) MUTATION ANALYSIS 50 (33%) 102 0.393
(1.00) 		0.058
(1.00) 		0.74
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.317
(1.00) 		0.179
(1.00) 		0.537
(1.00)
AMP PEAK 23(16P12 1) MUTATION ANALYSIS 40 (26%) 112 0.369
(1.00) 		0.746
(1.00) 		0.228
(1.00) 		0.0885
(1.00) 		0.0591
(1.00) 		0.236
(1.00) 		0.831
(1.00) 		0.383
(1.00) 		0.861
(1.00) 		0.957
(1.00)
AMP PEAK 24(17Q11 2) MUTATION ANALYSIS 69 (45%) 83 0.418
(1.00) 		0.201
(1.00) 		0.0312
(1.00) 		0.753
(1.00) 		0.00852
(1.00) 		0.139
(1.00) 		0.849
(1.00) 		0.00623
(1.00) 		0.883
(1.00) 		0.6
(1.00)
AMP PEAK 25(17Q12) MUTATION ANALYSIS 65 (43%) 87 0.186
(1.00) 		0.161
(1.00) 		0.192
(1.00) 		0.0608
(1.00) 		0.0734
(1.00) 		0.253
(1.00) 		0.849
(1.00) 		0.0432
(1.00) 		0.195
(1.00) 		0.795
(1.00)
AMP PEAK 26(19Q12) MUTATION ANALYSIS 65 (43%) 87 0.469
(1.00) 		0.861
(1.00) 		0.15
(1.00) 		0.204
(1.00) 		0.196
(1.00) 		0.823
(1.00) 		0.849
(1.00) 		0.328
(1.00) 		0.261
(1.00) 		0.163
(1.00)
AMP PEAK 27(19Q13 43) MUTATION ANALYSIS 63 (41%) 89 0.463
(1.00) 		0.916
(1.00) 		0.0932
(1.00) 		0.0182
(1.00) 		0.0553
(1.00) 		0.288
(1.00) 		0.702
(1.00) 		0.242
(1.00) 		0.403
(1.00) 		0.0708
(1.00)
AMP PEAK 28(20Q11 21) MUTATION ANALYSIS 106 (70%) 46 0.979
(1.00) 		0.217
(1.00) 		0.502
(1.00) 		0.449
(1.00) 		0.323
(1.00) 		0.674
(1.00) 		0.836
(1.00) 		0.251
(1.00) 		0.0127
(1.00) 		0.596
(1.00)
AMP PEAK 29(22Q11 23) MUTATION ANALYSIS 34 (22%) 118 0.26
(1.00) 		0.168
(1.00) 		0.479
(1.00) 		0.749
(1.00) 		0.977
(1.00) 		1
(1.00) 		0.251
(1.00) 		0.222
(1.00) 		0.706
(1.00) 		0.728
(1.00)
DEL PEAK 1(1P36 11) MUTATION ANALYSIS 30 (20%) 122 0.059
(1.00) 		0.0991
(1.00) 		0.741
(1.00) 		0.277
(1.00) 		0.0024
(1.00) 		0.93
(1.00) 		0.811
(1.00) 		0.996
(1.00) 		0.641
(1.00) 		0.243
(1.00)
DEL PEAK 2(1Q32 1) MUTATION ANALYSIS 31 (20%) 121 0.788
(1.00) 		0.101
(1.00) 		0.453
(1.00) 		0.5
(1.00) 		0.838
(1.00) 		0.93
(1.00) 		0.0562
(1.00) 		0.403
(1.00) 		0.00212
(1.00) 		0.386
(1.00)
DEL PEAK 3(2Q22 1) MUTATION ANALYSIS 46 (30%) 106 0.545
(1.00) 		0.954
(1.00) 		0.504
(1.00) 		0.966
(1.00) 		0.458
(1.00) 		0.594
(1.00) 		0.217
(1.00) 		0.332
(1.00) 		0.859
(1.00) 		0.665
(1.00)
DEL PEAK 4(2Q34) MUTATION ANALYSIS 66 (43%) 86 0.152
(1.00) 		0.0823
(1.00) 		0.72
(1.00) 		0.972
(1.00) 		0.658
(1.00) 		0.414
(1.00) 		0.849
(1.00) 		0.357
(1.00) 		0.426
(1.00) 		0.336
(1.00)
DEL PEAK 5(2Q37 1) MUTATION ANALYSIS 77 (51%) 75 0.136
(1.00) 		0.267
(1.00) 		0.44
(1.00) 		0.656
(1.00) 		0.328
(1.00) 		0.323
(1.00) 		0.0567
(1.00) 		0.179
(1.00) 		0.139
(1.00) 		0.977
(1.00)
DEL PEAK 6(3P21 31) MUTATION ANALYSIS 48 (32%) 104 0.879
(1.00) 		0.895
(1.00) 		0.879
(1.00) 		0.668
(1.00) 		0.682
(1.00) 		0.418
(1.00) 		0.541
(1.00) 		0.394
(1.00) 		0.67
(1.00) 		0.203
(1.00)
DEL PEAK 7(3P14 2) MUTATION ANALYSIS 48 (32%) 104 0.473
(1.00) 		0.884
(1.00) 		1
(1.00) 		0.65
(1.00) 		0.234
(1.00) 		0.336
(1.00) 		0.541
(1.00) 		0.245
(1.00) 		0.385
(1.00) 		0.0607
(1.00)
DEL PEAK 8(3P12 3) MUTATION ANALYSIS 42 (28%) 110 0.702
(1.00) 		0.146
(1.00) 		0.897
(1.00) 		0.508
(1.00) 		0.181
(1.00) 		0.137
(1.00) 		0.673
(1.00) 		0.0201
(1.00) 		0.744
(1.00) 		0.209
(1.00)
DEL PEAK 9(4Q22 1) MUTATION ANALYSIS 56 (37%) 96 0.449
(1.00) 		0.0638
(1.00) 		0.332
(1.00) 		0.0983
(1.00) 		0.323
(1.00) 		0.395
(1.00) 		0.324
(1.00) 		0.587
(1.00) 		0.71
(1.00) 		0.142
(1.00)
DEL PEAK 10(4Q34 2) MUTATION ANALYSIS 64 (42%) 88 0.513
(1.00) 		0.104
(1.00) 		0.283
(1.00) 		0.183
(1.00) 		0.438
(1.00) 		0.863
(1.00) 		0.703
(1.00) 		0.145
(1.00) 		0.932
(1.00) 		0.503
(1.00)
DEL PEAK 11(5Q11 2) MUTATION ANALYSIS 77 (51%) 75 0.6
(1.00) 		0.00141
(0.93) 		0.154
(1.00) 		0.479
(1.00) 		0.133
(1.00) 		0.144
(1.00) 		0.254
(1.00) 		0.083
(1.00) 		0.227
(1.00) 		0.319
(1.00)
DEL PEAK 12(5Q35 1) MUTATION ANALYSIS 74 (49%) 78 0.488
(1.00) 		0.0242
(1.00) 		0.122
(1.00) 		0.272
(1.00) 		0.227
(1.00) 		0.00853
(1.00) 		0.0902
(1.00) 		0.0331
(1.00) 		0.722
(1.00) 		0.224
(1.00)
DEL PEAK 13(6P25 3) MUTATION ANALYSIS 43 (28%) 109 0.223
(1.00) 		0.465
(1.00) 		0.0627
(1.00) 		0.00497
(1.00) 		0.0209
(1.00) 		0.666
(1.00) 		0.29
(1.00) 		0.0868
(1.00) 		0.434
(1.00) 		0.0942
(1.00)
DEL PEAK 14(6Q21) MUTATION ANALYSIS 66 (43%) 86 0.795
(1.00) 		0.045
(1.00) 		0.00142
(0.933) 		0.519
(1.00) 		0.009
(1.00) 		0.595
(1.00) 		0.849
(1.00) 		0.635
(1.00) 		0.792
(1.00) 		0.0044
(1.00)
DEL PEAK 15(6Q27) MUTATION ANALYSIS 66 (43%) 86 0.558
(1.00) 		0.111
(1.00) 		0.0153
(1.00) 		0.819
(1.00) 		0.0157
(1.00) 		0.595
(1.00) 		0.569
(1.00) 		0.268
(1.00) 		0.595
(1.00) 		0.00886
(1.00)
DEL PEAK 16(8P23 3) MUTATION ANALYSIS 81 (53%) 71 0.554
(1.00) 		0.25
(1.00) 		0.325
(1.00) 		0.537
(1.00) 		0.677
(1.00) 		0.0339
(1.00) 		0.254
(1.00) 		0.389
(1.00) 		0.702
(1.00) 		0.402
(1.00)
DEL PEAK 17(8P12) MUTATION ANALYSIS 72 (47%) 80 0.513
(1.00) 		0.0517
(1.00) 		0.857
(1.00) 		0.552
(1.00) 		0.974
(1.00) 		0.179
(1.00) 		0.131
(1.00) 		0.193
(1.00) 		0.732
(1.00) 		0.638
(1.00)
DEL PEAK 18(9P23) MUTATION ANALYSIS 68 (45%) 84 0.639
(1.00) 		0.413
(1.00) 		0.918
(1.00) 		0.653
(1.00) 		0.973
(1.00) 		0.79
(1.00) 		0.705
(1.00) 		0.864
(1.00) 		0.587
(1.00) 		0.713
(1.00)
DEL PEAK 19(9P21 3) MUTATION ANALYSIS 88 (58%) 64 0.841
(1.00) 		0.145
(1.00) 		0.927
(1.00) 		0.304
(1.00) 		0.336
(1.00) 		0.863
(1.00) 		0.847
(1.00) 		0.74
(1.00) 		0.331
(1.00) 		0.666
(1.00)
DEL PEAK 20(9Q22 33) MUTATION ANALYSIS 60 (39%) 92 0.731
(1.00) 		0.241
(1.00) 		0.708
(1.00) 		0.705
(1.00) 		0.504
(1.00) 		0.747
(1.00) 		0.439
(1.00) 		0.622
(1.00) 		0.0858
(1.00) 		0.743
(1.00)
DEL PEAK 21(10P11 22) MUTATION ANALYSIS 32 (21%) 120 0.901
(1.00) 		0.189
(1.00) 		0.922
(1.00) 		0.738
(1.00) 		0.217
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.191
(1.00) 		0.984
(1.00) 		0.424
(1.00)
DEL PEAK 22(10Q23 31) MUTATION ANALYSIS 64 (42%) 88 0.581
(1.00) 		0.00823
(1.00) 		0.304
(1.00) 		0.554
(1.00) 		0.11
(1.00) 		0.432
(1.00) 		0.703
(1.00) 		0.00638
(1.00) 		0.46
(1.00) 		0.203
(1.00)
DEL PEAK 23(11P15 5) MUTATION ANALYSIS 74 (49%) 78 0.214
(1.00) 		0.00802
(1.00) 		0.0197
(1.00) 		0.57
(1.00) 		0.0481
(1.00) 		0.411
(1.00) 		0.851
(1.00) 		0.089
(1.00) 		0.733
(1.00) 		0.152
(1.00)
DEL PEAK 24(11Q25) MUTATION ANALYSIS 49 (32%) 103 0.357
(1.00) 		0.293
(1.00) 		0.408
(1.00) 		0.0877
(1.00) 		0.305
(1.00) 		0.486
(1.00) 		0.842
(1.00) 		0.551
(1.00) 		0.172
(1.00) 		0.0353
(1.00)
DEL PEAK 25(13Q14 2) MUTATION ANALYSIS 61 (40%) 91 0.119
(1.00) 		0.0149
(1.00) 		0.108
(1.00) 		0.689
(1.00) 		0.112
(1.00) 		0.82
(1.00) 		0.243
(1.00) 		0.339
(1.00) 		0.348
(1.00) 		0.303
(1.00)
DEL PEAK 26(14Q12) MUTATION ANALYSIS 45 (30%) 107 0.52
(1.00) 		0.0629
(1.00) 		0.246
(1.00) 		0.641
(1.00) 		0.07
(1.00) 		0.892
(1.00) 		0.303
(1.00) 		0.617
(1.00) 		0.0884
(1.00) 		0.218
(1.00)
DEL PEAK 27(14Q24 1) MUTATION ANALYSIS 46 (30%) 106 0.554
(1.00) 		0.201
(1.00) 		0.585
(1.00) 		0.845
(1.00) 		0.105
(1.00) 		0.673
(1.00) 		0.146
(1.00) 		0.918
(1.00) 		0.203
(1.00) 		0.541
(1.00)
DEL PEAK 28(15Q13 1) MUTATION ANALYSIS 58 (38%) 94 0.188
(1.00) 		0.0607
(1.00) 		0.663
(1.00) 		0.437
(1.00) 		0.504
(1.00) 		0.0947
(1.00) 		0.33
(1.00) 		0.156
(1.00) 		0.899
(1.00) 		0.43
(1.00)
DEL PEAK 29(16P13 3) MUTATION ANALYSIS 57 (38%) 95 0.652
(1.00) 		0.0709
(1.00) 		0.492
(1.00) 		0.175
(1.00) 		0.523
(1.00) 		0.496
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.965
(1.00) 		0.581
(1.00)
DEL PEAK 30(16Q23 1) MUTATION ANALYSIS 44 (29%) 108 0.922
(1.00) 		0.527
(1.00) 		0.463
(1.00) 		0.839
(1.00) 		0.1
(1.00) 		0.403
(1.00) 		0.401
(1.00) 		0.0277
(1.00) 		0.593
(1.00) 		0.245
(1.00)
DEL PEAK 31(17P12) MUTATION ANALYSIS 79 (52%) 73 0.433
(1.00) 		0.0989
(1.00) 		0.0107
(1.00) 		0.972
(1.00) 		0.0969
(1.00) 		1
(1.00) 		0.569
(1.00) 		0.427
(1.00) 		0.778
(1.00) 		0.613
(1.00)
DEL PEAK 32(18Q23) MUTATION ANALYSIS 65 (43%) 87 0.198
(1.00) 		0.0824
(1.00) 		0.85
(1.00) 		0.164
(1.00) 		0.805
(1.00) 		0.539
(1.00) 		0.34
(1.00) 		0.419
(1.00) 		0.647
(1.00) 		0.401
(1.00)
DEL PEAK 33(19P13 3) MUTATION ANALYSIS 58 (38%) 94 0.572
(1.00) 		0.2
(1.00) 		0.0697
(1.00) 		0.287
(1.00) 		0.0481
(1.00) 		0.0139
(1.00) 		1
(1.00) 		0.0865
(1.00) 		0.123
(1.00) 		0.583
(1.00)
DEL PEAK 34(22Q13 31) MUTATION ANALYSIS 60 (39%) 92 0.88
(1.00) 		0.319
(1.00) 		0.449
(1.00) 		0.658
(1.00) 		0.551
(1.00) 		0.0374
(1.00) 		0.846
(1.00) 		0.062
(1.00) 		0.279
(1.00) 		0.364
(1.00)
DEL PEAK 35(XP11 3) MUTATION ANALYSIS 40 (26%) 112 0.862
(1.00) 		0.162
(1.00) 		0.479
(1.00) 		0.676
(1.00) 		0.902
(1.00) 		0.94
(1.00) 		0.387
(1.00) 		0.95
(1.00) 		0.286
(1.00) 		0.949
(1.00)
DEL PEAK 36(XQ21 33) MUTATION ANALYSIS 34 (22%) 118 0.938
(1.00) 		0.982
(1.00) 		0.744
(1.00) 		0.365
(1.00) 		0.802
(1.00) 		0.352
(1.00) 		1
(1.00) 		0.48
(1.00) 		0.64
(1.00) 		0.86
(1.00)
DEL PEAK 37(XQ23) MUTATION ANALYSIS 33 (22%) 119 0.616
(1.00) 		0.714
(1.00) 		0.939
(1.00) 		0.738
(1.00) 		0.499
(1.00) 		0.265
(1.00) 		0.819
(1.00) 		0.812
(1.00) 		0.818
(1.00) 		0.995
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 152

  • Number of significantly focal cnvs = 66

  • Number of selected clinical features = 10

  • 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

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] 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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