Correlation between copy number variations of arm-level result and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1W37TN8
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1W37TN8
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 80 arm-level events and 8 clinical features across 117 patients, one significant finding detected with Q value < 0.25.

  • 11Q GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER COMPLETENESS
OF
RESECTION
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 Fisher's exact test
11Q GAIN MUTATION ANALYSIS 4 (3%) 113 0.109
(1.00) 		0.79
(1.00) 		0.000293
(0.188) 		0.57
(1.00) 		1
(1.00) 		0.0971
(1.00) 		0.296
(1.00) 		0.0275
(1.00)
1P GAIN MUTATION ANALYSIS 17 (15%) 100 0.587
(1.00) 		0.658
(1.00) 		0.802
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.652
(1.00) 		0.591
(1.00) 		0.271
(1.00)
1Q GAIN MUTATION ANALYSIS 64 (55%) 53 0.167
(1.00) 		0.827
(1.00) 		0.0574
(1.00) 		0.0763
(1.00) 		0.106
(1.00) 		0.63
(1.00) 		0.13
(1.00) 		1
(1.00)
2P GAIN MUTATION ANALYSIS 18 (15%) 99 0.773
(1.00) 		0.421
(1.00) 		0.0853
(1.00) 		0.379
(1.00) 		0.0519
(1.00) 		0.368
(1.00) 		0.114
(1.00) 		0.127
(1.00)
2Q GAIN MUTATION ANALYSIS 15 (13%) 102 0.853
(1.00) 		0.477
(1.00) 		0.152
(1.00) 		0.817
(1.00) 		0.345
(1.00) 		0.31
(1.00) 		0.0846
(1.00) 		0.271
(1.00)
3P GAIN MUTATION ANALYSIS 8 (7%) 109 0.0367
(1.00) 		0.771
(1.00) 		0.843
(1.00) 		0.362
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.587
(1.00)
3Q GAIN MUTATION ANALYSIS 9 (8%) 108 0.0122
(1.00) 		0.689
(1.00) 		0.843
(1.00) 		0.578
(1.00) 		0.15
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.64
(1.00)
4P GAIN MUTATION ANALYSIS 8 (7%) 109 0.389
(1.00) 		0.327
(1.00) 		0.998
(1.00) 		0.935
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.427
(1.00)
4Q GAIN MUTATION ANALYSIS 3 (3%) 114 0.871
(1.00) 		0.501
(1.00) 		0.99
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0928
(1.00)
5P GAIN MUTATION ANALYSIS 47 (40%) 70 0.904
(1.00) 		0.184
(1.00) 		0.552
(1.00) 		0.347
(1.00) 		0.286
(1.00) 		0.409
(1.00) 		0.847
(1.00) 		1
(1.00)
5Q GAIN MUTATION ANALYSIS 36 (31%) 81 0.989
(1.00) 		0.342
(1.00) 		0.711
(1.00) 		0.798
(1.00) 		0.553
(1.00) 		0.909
(1.00) 		0.311
(1.00) 		0.719
(1.00)
6P GAIN MUTATION ANALYSIS 29 (25%) 88 0.203
(1.00) 		0.545
(1.00) 		0.413
(1.00) 		1
(1.00) 		1
(1.00) 		0.0908
(1.00) 		1
(1.00) 		0.458
(1.00)
6Q GAIN MUTATION ANALYSIS 17 (15%) 100 0.229
(1.00) 		0.245
(1.00) 		0.0785
(1.00) 		0.814
(1.00) 		1
(1.00) 		0.0172
(1.00) 		0.591
(1.00) 		0.0981
(1.00)
7P GAIN MUTATION ANALYSIS 37 (32%) 80 0.979
(1.00) 		0.0481
(1.00) 		0.563
(1.00) 		0.381
(1.00) 		0.195
(1.00) 		0.828
(1.00) 		0.685
(1.00) 		0.613
(1.00)
7Q GAIN MUTATION ANALYSIS 39 (33%) 78 0.855
(1.00) 		0.163
(1.00) 		0.418
(1.00) 		0.365
(1.00) 		0.211
(1.00) 		0.535
(1.00) 		0.842
(1.00) 		0.898
(1.00)
8P GAIN MUTATION ANALYSIS 22 (19%) 95 0.821
(1.00) 		0.149
(1.00) 		0.468
(1.00) 		0.647
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.0499
(1.00) 		0.0912
(1.00)
8Q GAIN MUTATION ANALYSIS 56 (48%) 61 0.897
(1.00) 		0.773
(1.00) 		0.288
(1.00) 		0.514
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.00797
(1.00) 		0.83
(1.00)
9P GAIN MUTATION ANALYSIS 4 (3%) 113 0.819
(1.00) 		0.99
(1.00) 		0.369
(1.00) 		0.745
(1.00) 		1
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.321
(1.00)
9Q GAIN MUTATION ANALYSIS 4 (3%) 113 0.16
(1.00) 		0.855
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.149
(1.00) 		0.321
(1.00)
10P GAIN MUTATION ANALYSIS 17 (15%) 100 0.408
(1.00) 		0.197
(1.00) 		0.337
(1.00) 		0.564
(1.00) 		1
(1.00) 		0.291
(1.00) 		1
(1.00) 		1
(1.00)
10Q GAIN MUTATION ANALYSIS 10 (9%) 107 0.786
(1.00) 		0.677
(1.00) 		0.196
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.499
(1.00) 		0.686
(1.00)
11P GAIN MUTATION ANALYSIS 5 (4%) 112 0.14
(1.00) 		0.519
(1.00) 		0.00393
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.0561
(1.00) 		0.155
(1.00) 		0.0396
(1.00)
12P GAIN MUTATION ANALYSIS 8 (7%) 109 0.76
(1.00) 		0.241
(1.00) 		0.809
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.528
(1.00)
12Q GAIN MUTATION ANALYSIS 12 (10%) 105 0.461
(1.00) 		0.152
(1.00) 		0.109
(1.00) 		0.882
(1.00) 		0.315
(1.00) 		0.564
(1.00) 		0.13
(1.00) 		0.699
(1.00)
13Q GAIN MUTATION ANALYSIS 9 (8%) 108 0.161
(1.00) 		0.255
(1.00) 		0.762
(1.00) 		0.942
(1.00) 		0.15
(1.00) 		0.729
(1.00) 		0.727
(1.00) 		0.587
(1.00)
14Q GAIN MUTATION ANALYSIS 8 (7%) 109 0.999
(1.00) 		0.994
(1.00) 		0.086
(1.00) 		1
(1.00) 		1
(1.00) 		0.0972
(1.00) 		0.708
(1.00) 		0.0677
(1.00)
15Q GAIN MUTATION ANALYSIS 10 (9%) 107 0.862
(1.00) 		0.4
(1.00) 		0.963
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.541
(1.00) 		1
(1.00) 		1
(1.00)
16P GAIN MUTATION ANALYSIS 11 (9%) 106 0.906
(1.00) 		0.52
(1.00) 		0.218
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.756
(1.00) 		1
(1.00) 		1
(1.00)
16Q GAIN MUTATION ANALYSIS 4 (3%) 113 0.795
(1.00) 		0.371
(1.00) 		0.891
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
17P GAIN MUTATION ANALYSIS 10 (9%) 107 0.321
(1.00) 		0.82
(1.00) 		0.0654
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.541
(1.00) 		0.741
(1.00) 		0.407
(1.00)
17Q GAIN MUTATION ANALYSIS 36 (31%) 81 0.183
(1.00) 		0.454
(1.00) 		0.052
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.68
(1.00) 		0.231
(1.00)
18P GAIN MUTATION ANALYSIS 9 (8%) 108 0.345
(1.00) 		0.349
(1.00) 		0.0672
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.0501
(1.00)
18Q GAIN MUTATION ANALYSIS 9 (8%) 108 0.345
(1.00) 		0.349
(1.00) 		0.0672
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.0501
(1.00)
19P GAIN MUTATION ANALYSIS 27 (23%) 90 0.482
(1.00) 		0.739
(1.00) 		0.00294
(1.00) 		0.0108
(1.00) 		0.532
(1.00) 		0.0595
(1.00) 		0.258
(1.00) 		0.261
(1.00)
19Q GAIN MUTATION ANALYSIS 29 (25%) 88 0.491
(1.00) 		0.929
(1.00) 		0.00634
(1.00) 		0.029
(1.00) 		0.532
(1.00) 		0.0689
(1.00) 		0.19
(1.00) 		0.231
(1.00)
20P GAIN MUTATION ANALYSIS 34 (29%) 83 0.226
(1.00) 		0.557
(1.00) 		0.641
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.403
(1.00) 		0.441
(1.00)
20Q GAIN MUTATION ANALYSIS 36 (31%) 81 0.285
(1.00) 		0.565
(1.00) 		0.722
(1.00) 		0.955
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.544
(1.00) 		0.302
(1.00)
21Q GAIN MUTATION ANALYSIS 10 (9%) 107 0.563
(1.00) 		0.756
(1.00) 		0.425
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		0.174
(1.00) 		0.216
(1.00)
22Q GAIN MUTATION ANALYSIS 16 (14%) 101 0.915
(1.00) 		0.528
(1.00) 		0.78
(1.00) 		0.681
(1.00) 		0.374
(1.00) 		0.812
(1.00) 		1
(1.00) 		0.201
(1.00)
XQ GAIN MUTATION ANALYSIS 24 (21%) 93 0.195
(1.00) 		0.0205
(1.00) 		0.659
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.479
(1.00) 		0.917
(1.00)
1P LOSS MUTATION ANALYSIS 28 (24%) 89 0.749
(1.00) 		0.796
(1.00) 		0.15
(1.00) 		0.944
(1.00) 		0.149
(1.00) 		0.0979
(1.00) 		0.512
(1.00) 		0.0361
(1.00)
1Q LOSS MUTATION ANALYSIS 12 (10%) 105 0.332
(1.00) 		0.16
(1.00) 		0.214
(1.00) 		0.705
(1.00) 		0.0272
(1.00) 		0.776
(1.00) 		0.762
(1.00) 		0.289
(1.00)
2P LOSS MUTATION ANALYSIS 8 (7%) 109 0.289
(1.00) 		0.902
(1.00) 		0.837
(1.00) 		0.118
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.427
(1.00)
2Q LOSS MUTATION ANALYSIS 10 (9%) 107 0.888
(1.00) 		0.829
(1.00) 		0.924
(1.00) 		0.425
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.266
(1.00)
3P LOSS MUTATION ANALYSIS 14 (12%) 103 0.0909
(1.00) 		0.931
(1.00) 		0.109
(1.00) 		0.138
(1.00) 		0.374
(1.00) 		0.228
(1.00) 		0.381
(1.00) 		0.662
(1.00)
3Q LOSS MUTATION ANALYSIS 6 (5%) 111 0.0392
(1.00) 		0.0969
(1.00) 		0.652
(1.00) 		0.627
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.671
(1.00) 		1
(1.00)
4P LOSS MUTATION ANALYSIS 28 (24%) 89 1
(1.00) 		0.765
(1.00) 		0.162
(1.00) 		0.919
(1.00) 		0.121
(1.00) 		0.0979
(1.00) 		0.512
(1.00) 		0.367
(1.00)
4Q LOSS MUTATION ANALYSIS 37 (32%) 80 0.85
(1.00) 		0.856
(1.00) 		0.459
(1.00) 		0.779
(1.00) 		0.228
(1.00) 		0.177
(1.00) 		0.838
(1.00) 		0.31
(1.00)
5P LOSS MUTATION ANALYSIS 9 (8%) 108 0.442
(1.00) 		0.911
(1.00) 		0.387
(1.00) 		0.763
(1.00) 		0.219
(1.00) 		1
(1.00) 		0.48
(1.00) 		0.491
(1.00)
5Q LOSS MUTATION ANALYSIS 13 (11%) 104 0.174
(1.00) 		0.714
(1.00) 		0.621
(1.00) 		0.329
(1.00) 		0.252
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00)
6P LOSS MUTATION ANALYSIS 13 (11%) 104 0.697
(1.00) 		0.983
(1.00) 		0.977
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.0911
(1.00) 		1
(1.00) 		1
(1.00)
6Q LOSS MUTATION ANALYSIS 35 (30%) 82 0.668
(1.00) 		0.0536
(1.00) 		0.5
(1.00) 		0.881
(1.00) 		0.195
(1.00) 		0.337
(1.00) 		0.298
(1.00) 		0.941
(1.00)
7P LOSS MUTATION ANALYSIS 8 (7%) 109 0.427
(1.00) 		0.615
(1.00) 		0.85
(1.00) 		0.381
(1.00) 		1
(1.00) 		1
(1.00) 		0.0513
(1.00) 		0.587
(1.00)
7Q LOSS MUTATION ANALYSIS 11 (9%) 106 0.367
(1.00) 		0.845
(1.00) 		0.876
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.0192
(1.00) 		0.378
(1.00)
8P LOSS MUTATION ANALYSIS 56 (48%) 61 0.0881
(1.00) 		0.00114
(0.726) 		0.319
(1.00) 		0.258
(1.00) 		0.0555
(1.00) 		0.375
(1.00) 		0.567
(1.00) 		0.321
(1.00)
8Q LOSS MUTATION ANALYSIS 14 (12%) 103 0.74
(1.00) 		0.408
(1.00) 		0.0244
(1.00) 		0.00297
(1.00) 		0.252
(1.00) 		0.105
(1.00) 		0.143
(1.00) 		1
(1.00)
9P LOSS MUTATION ANALYSIS 36 (31%) 81 0.265
(1.00) 		0.87
(1.00) 		0.0724
(1.00) 		0.235
(1.00) 		0.245
(1.00) 		0.0886
(1.00) 		0.311
(1.00) 		0.0625
(1.00)
9Q LOSS MUTATION ANALYSIS 37 (32%) 80 0.06
(1.00) 		0.898
(1.00) 		0.0517
(1.00) 		0.603
(1.00) 		0.0277
(1.00) 		0.0325
(1.00) 		0.838
(1.00) 		0.0542
(1.00)
10P LOSS MUTATION ANALYSIS 13 (11%) 104 0.84
(1.00) 		0.0441
(1.00) 		0.0847
(1.00) 		0.355
(1.00) 		0.315
(1.00) 		0.787
(1.00) 		0.365
(1.00) 		1
(1.00)
10Q LOSS MUTATION ANALYSIS 26 (22%) 91 0.0887
(1.00) 		0.721
(1.00) 		0.355
(1.00) 		0.325
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.549
(1.00)
11P LOSS MUTATION ANALYSIS 20 (17%) 97 0.902
(1.00) 		0.00271
(1.00) 		0.321
(1.00) 		0.469
(1.00) 		0.0519
(1.00) 		0.84
(1.00) 		0.805
(1.00) 		0.668
(1.00)
11Q LOSS MUTATION ANALYSIS 22 (19%) 95 0.978
(1.00) 		0.0154
(1.00) 		0.286
(1.00) 		0.326
(1.00) 		0.0722
(1.00) 		0.715
(1.00) 		1
(1.00) 		0.277
(1.00)
12P LOSS MUTATION ANALYSIS 21 (18%) 96 0.147
(1.00) 		0.672
(1.00) 		0.345
(1.00) 		0.862
(1.00) 		0.0833
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.151
(1.00)
12Q LOSS MUTATION ANALYSIS 12 (10%) 105 0.615
(1.00) 		0.302
(1.00) 		0.136
(1.00) 		1
(1.00) 		1
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.105
(1.00)
13Q LOSS MUTATION ANALYSIS 40 (34%) 77 0.786
(1.00) 		0.0861
(1.00) 		0.3
(1.00) 		0.0423
(1.00) 		1
(1.00) 		0.417
(1.00) 		0.841
(1.00) 		0.233
(1.00)
14Q LOSS MUTATION ANALYSIS 38 (32%) 79 0.848
(1.00) 		0.768
(1.00) 		0.116
(1.00) 		0.0415
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.685
(1.00) 		0.174
(1.00)
15Q LOSS MUTATION ANALYSIS 22 (19%) 95 0.399
(1.00) 		0.508
(1.00) 		0.513
(1.00) 		0.357
(1.00) 		0.0952
(1.00) 		0.208
(1.00) 		0.333
(1.00) 		0.912
(1.00)
16P LOSS MUTATION ANALYSIS 33 (28%) 84 0.083
(1.00) 		0.368
(1.00) 		0.149
(1.00) 		0.41
(1.00) 		0.245
(1.00) 		0.203
(1.00) 		0.834
(1.00) 		0.0722
(1.00)
16Q LOSS MUTATION ANALYSIS 43 (37%) 74 0.208
(1.00) 		0.31
(1.00) 		0.439
(1.00) 		0.526
(1.00) 		0.573
(1.00) 		0.275
(1.00) 		0.554
(1.00) 		0.0737
(1.00)
17P LOSS MUTATION ANALYSIS 58 (50%) 59 0.346
(1.00) 		0.158
(1.00) 		0.134
(1.00) 		0.515
(1.00) 		0.251
(1.00) 		0.271
(1.00) 		0.849
(1.00) 		0.0781
(1.00)
17Q LOSS MUTATION ANALYSIS 9 (8%) 108 0.573
(1.00) 		0.0433
(1.00) 		0.0353
(1.00) 		0.502
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.727
(1.00) 		1
(1.00)
18P LOSS MUTATION ANALYSIS 18 (15%) 99 0.242
(1.00) 		0.365
(1.00) 		0.966
(1.00) 		0.915
(1.00) 		0.374
(1.00) 		0.828
(1.00) 		0.599
(1.00) 		1
(1.00)
18Q LOSS MUTATION ANALYSIS 19 (16%) 98 0.481
(1.00) 		0.161
(1.00) 		0.487
(1.00) 		0.978
(1.00) 		0.374
(1.00) 		0.32
(1.00) 		0.195
(1.00) 		1
(1.00)
19P LOSS MUTATION ANALYSIS 14 (12%) 103 0.0753
(1.00) 		0.705
(1.00) 		0.956
(1.00) 		0.732
(1.00) 		0.315
(1.00) 		0.792
(1.00) 		0.564
(1.00) 		0.0712
(1.00)
19Q LOSS MUTATION ANALYSIS 10 (9%) 107 0.293
(1.00) 		0.616
(1.00) 		0.948
(1.00) 		0.906
(1.00) 		0.252
(1.00) 		0.739
(1.00) 		0.741
(1.00) 		0.178
(1.00)
20P LOSS MUTATION ANALYSIS 7 (6%) 110 0.765
(1.00) 		0.237
(1.00) 		0.512
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20Q LOSS MUTATION ANALYSIS 4 (3%) 113 0.246
(1.00) 		0.911
(1.00) 		0.0631
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.631
(1.00) 		1
(1.00)
21Q LOSS MUTATION ANALYSIS 29 (25%) 88 0.0522
(1.00) 		0.503
(1.00) 		0.0816
(1.00) 		0.313
(1.00) 		0.135
(1.00) 		0.103
(1.00) 		0.0141
(1.00) 		0.31
(1.00)
22Q LOSS MUTATION ANALYSIS 20 (17%) 97 0.196
(1.00) 		0.741
(1.00) 		0.92
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.217
(1.00) 		0.0175
(1.00)
XQ LOSS MUTATION ANALYSIS 16 (14%) 101 0.437
(1.00) 		0.716
(1.00) 		0.71
(1.00) 		0.122
(1.00) 		0.345
(1.00) 		0.64
(1.00) 		0.782
(1.00) 		0.269
(1.00)
'11Q GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000293 (Chi-square test), Q value = 0.19

Table S1.  Gene #22: '11Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 45 25 2 25 3 4 1 1 1
11Q GAIN MUTATED 3 0 0 0 0 0 1 0 0
11Q GAIN WILD-TYPE 42 25 2 25 3 4 0 1 1

Figure S1.  Get High-res Image Gene #22: '11Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input

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

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

  • Number of patients = 117

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 8

  • Exclude regions 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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