Correlation between copy number variations of arm-level result and selected clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1TT4PK6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1TT4PK6
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 9 clinical features across 150 patients, 2 significant findings detected with Q value < 0.25.

  • 2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 16q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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 9 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 PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test t-test
2p loss 8 (5%) 142 0.571
(1.00) 		0.307
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.73
(1.00) 		0.308
(1.00) 		0.621
(1.00) 		2.9e-05
(0.0198)
16q loss 21 (14%) 129 0.48
(1.00) 		0.0628
(1.00) 		0.388
(1.00) 		0.171
(1.00) 		0.871
(1.00) 		0.000101
(0.0685) 		1
(1.00) 		0.668
(1.00) 		0.732
(1.00)
1p gain 45 (30%) 105 0.84
(1.00) 		0.116
(1.00) 		0.494
(1.00) 		0.655
(1.00) 		0.68
(1.00) 		0.284
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.35
(1.00)
1q gain 73 (49%) 77 0.549
(1.00) 		0.687
(1.00) 		0.21
(1.00) 		0.683
(1.00) 		0.729
(1.00) 		0.916
(1.00) 		0.274
(1.00) 		0.899
(1.00) 		0.6
(1.00)
2p gain 26 (17%) 124 0.144
(1.00) 		0.329
(1.00) 		1
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.92
(1.00)
2q gain 18 (12%) 132 0.00737
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.841
(1.00) 		0.739
(1.00) 		0.651
(1.00)
3p gain 37 (25%) 113 0.0215
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.445
(1.00) 		0.432
(1.00) 		0.117
(1.00)
3q gain 89 (59%) 61 0.475
(1.00) 		0.832
(1.00) 		0.674
(1.00) 		0.0658
(1.00) 		0.0939
(1.00) 		0.082
(1.00) 		0.0255
(1.00) 		0.543
(1.00) 		0.0134
(1.00)
4p gain 3 (2%) 147 0.193
(1.00) 		0.33
(1.00) 		0.986
(1.00) 		0.424
(1.00)
4q gain 4 (3%) 146 0.85
(1.00) 		0.0244
(1.00) 		0.557
(1.00) 		0.253
(1.00) 		0.166
(1.00) 		0.955
(1.00) 		1
(1.00) 		0.551
(1.00)
5p gain 51 (34%) 99 0.63
(1.00) 		0.284
(1.00) 		0.641
(1.00) 		0.501
(1.00) 		0.737
(1.00) 		0.333
(1.00) 		0.355
(1.00) 		0.287
(1.00) 		0.594
(1.00)
5q gain 22 (15%) 128 0.387
(1.00) 		0.17
(1.00) 		1
(1.00) 		1
(1.00) 		0.599
(1.00) 		0.778
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.44
(1.00)
6p gain 31 (21%) 119 0.498
(1.00) 		0.823
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.868
(1.00) 		0.416
(1.00) 		0.764
(1.00) 		0.524
(1.00)
6q gain 17 (11%) 133 0.153
(1.00) 		0.891
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.111
(1.00) 		0.727
(1.00) 		0.164
(1.00) 		0.461
(1.00) 		0.316
(1.00)
7p gain 16 (11%) 134 0.968
(1.00) 		0.318
(1.00) 		0.269
(1.00) 		1
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.732
(1.00) 		0.577
(1.00)
7q gain 15 (10%) 135 0.294
(1.00) 		0.0976
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.624
(1.00) 		0.135
(1.00) 		0.0682
(1.00)
8p gain 24 (16%) 126 0.448
(1.00) 		0.0223
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		0.802
(1.00) 		0.555
(1.00) 		0.68
(1.00) 		0.522
(1.00)
8q gain 41 (27%) 109 0.757
(1.00) 		0.0366
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.556
(1.00) 		0.253
(1.00) 		0.465
(1.00) 		0.289
(1.00) 		0.941
(1.00)
9p gain 18 (12%) 132 0.945
(1.00) 		0.973
(1.00) 		0.513
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.31
(1.00) 		0.434
(1.00) 		0.7
(1.00)
9q gain 20 (13%) 130 0.982
(1.00) 		0.815
(1.00) 		0.534
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.199
(1.00) 		0.687
(1.00) 		0.7
(1.00)
10p gain 11 (7%) 139 0.692
(1.00) 		0.393
(1.00) 		0.441
(1.00) 		0.153
(1.00) 		0.608
(1.00) 		0.969
(1.00) 		1
(1.00) 		0.342
(1.00)
10q gain 6 (4%) 144 0.814
(1.00) 		0.46
(1.00) 		0.318
(1.00) 		0.598
(1.00) 		0.21
(1.00) 		0.987
(1.00) 		1
(1.00) 		0.508
(1.00)
11p gain 4 (3%) 146 0.255
(1.00) 		0.09
(1.00) 		0.0212
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.522
(1.00) 		0.344
(1.00)
11q gain 4 (3%) 146 0.266
(1.00) 		0.265
(1.00) 		0.068
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.522
(1.00) 		0.344
(1.00)
12p gain 22 (15%) 128 0.234
(1.00) 		0.0193
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.21
(1.00) 		0.062
(1.00) 		0.296
(1.00)
12q gain 22 (15%) 128 0.4
(1.00) 		0.0057
(1.00) 		0.771
(1.00) 		1
(1.00) 		1
(1.00) 		0.679
(1.00) 		0.21
(1.00) 		0.0932
(1.00) 		0.399
(1.00)
13q gain 13 (9%) 137 0.482
(1.00) 		0.974
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.189
(1.00)
14q gain 21 (14%) 129 0.895
(1.00) 		0.615
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.646
(1.00) 		0.401
(1.00) 		0.755
(1.00) 		0.751
(1.00) 		0.167
(1.00)
15q gain 23 (15%) 127 0.0299
(1.00) 		0.958
(1.00) 		0.215
(1.00) 		1
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.223
(1.00) 		0.00638
(1.00) 		0.791
(1.00)
16p gain 20 (13%) 130 0.962
(1.00) 		0.893
(1.00) 		0.561
(1.00) 		0.391
(1.00) 		0.871
(1.00) 		0.922
(1.00) 		0.747
(1.00) 		0.534
(1.00) 		0.819
(1.00)
16q gain 17 (11%) 133 0.0627
(1.00) 		0.563
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.85
(1.00) 		0.487
(1.00) 		0.862
(1.00) 		0.305
(1.00)
17p gain 11 (7%) 139 0.805
(1.00) 		0.31
(1.00) 		0.0529
(1.00) 		0.0146
(1.00) 		0.541
(1.00) 		0.922
(1.00) 		0.0876
(1.00) 		0.172
(1.00)
17q gain 21 (14%) 129 0.999
(1.00) 		0.974
(1.00) 		0.00839
(1.00) 		0.0585
(1.00) 		0.856
(1.00) 		0.662
(1.00) 		0.755
(1.00) 		0.137
(1.00)
18p gain 18 (12%) 132 0.592
(1.00) 		0.043
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.841
(1.00) 		0.185
(1.00) 		0.914
(1.00) 		0.67
(1.00)
18q gain 8 (5%) 142 0.724
(1.00) 		0.00961
(1.00) 		0.137
(1.00) 		0.598
(1.00) 		0.448
(1.00) 		0.88
(1.00) 		0.129
(1.00) 		0.164
(1.00)
19p gain 21 (14%) 129 0.723
(1.00) 		0.729
(1.00) 		0.382
(1.00) 		0.0348
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.0514
(1.00) 		0.549
(1.00) 		0.722
(1.00)
19q gain 32 (21%) 118 0.0378
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.029
(1.00) 		0.352
(1.00) 		0.893
(1.00)
20p gain 48 (32%) 102 0.991
(1.00) 		0.365
(1.00) 		0.817
(1.00) 		0.0424
(1.00) 		0.739
(1.00) 		0.814
(1.00) 		0.644
(1.00) 		0.927
(1.00) 		0.264
(1.00)
20q gain 54 (36%) 96 0.58
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.383
(1.00) 		0.534
(1.00) 		0.841
(1.00) 		0.654
(1.00) 		0.764
(1.00) 		0.593
(1.00)
21q gain 19 (13%) 131 0.00175
(1.00) 		0.0516
(1.00) 		1
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.472
(1.00) 		0.0929
(1.00) 		0.558
(1.00) 		0.941
(1.00)
22q gain 18 (12%) 132 0.192
(1.00) 		0.0621
(1.00) 		0.316
(1.00) 		0.727
(1.00) 		0.834
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.576
(1.00)
xq gain 19 (13%) 131 0.161
(1.00) 		0.549
(1.00) 		0.344
(1.00) 		0.526
(1.00) 		0.599
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.96
(1.00) 		0.955
(1.00)
1p loss 6 (4%) 144 0.59
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.987
(1.00) 		0.262
(1.00)
1q loss 6 (4%) 144 0.764
(1.00) 		0.472
(1.00) 		0.576
(1.00) 		0.104
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.0585
(1.00) 		0.636
(1.00)
2q loss 15 (10%) 135 0.661
(1.00) 		0.519
(1.00) 		0.738
(1.00) 		1
(1.00) 		1
(1.00) 		0.467
(1.00) 		0.135
(1.00) 		0.781
(1.00)
3p loss 39 (26%) 111 0.513
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.00844
(1.00) 		0.724
(1.00) 		0.0504
(1.00) 		0.0429
(1.00) 		0.775
(1.00) 		0.44
(1.00)
3q loss 5 (3%) 145 0.624
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.955
(1.00) 		0.59
(1.00)
4p loss 62 (41%) 88 0.603
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.0402
(1.00) 		0.448
(1.00) 		0.0328
(1.00) 		0.122
(1.00) 		0.859
(1.00) 		0.296
(1.00)
4q loss 40 (27%) 110 0.0105
(1.00) 		0.554
(1.00) 		0.461
(1.00) 		0.0294
(1.00) 		0.923
(1.00) 		0.484
(1.00) 		0.62
(1.00) 		0.865
(1.00) 		0.219
(1.00)
5p loss 12 (8%) 138 0.00146
(0.996) 		0.578
(1.00) 		0.441
(1.00) 		0.0569
(1.00) 		1
(1.00) 		0.957
(1.00) 		0.0301
(1.00) 		0.987
(1.00) 		0.301
(1.00)
5q loss 32 (21%) 118 0.257
(1.00) 		0.239
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.541
(1.00) 		0.182
(1.00) 		0.756
(1.00) 		0.503
(1.00)
6p loss 19 (13%) 131 0.726
(1.00) 		0.44
(1.00) 		0.722
(1.00) 		0.293
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.201
(1.00) 		0.482
(1.00) 		0.878
(1.00)
6q loss 35 (23%) 115 0.108
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.113
(1.00) 		0.464
(1.00) 		0.66
(1.00) 		0.442
(1.00) 		0.0102
(1.00) 		0.624
(1.00)
7p loss 16 (11%) 134 0.234
(1.00) 		0.716
(1.00) 		0.503
(1.00) 		0.293
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.00106
(0.721) 		0.38
(1.00) 		0.303
(1.00)
7q loss 25 (17%) 125 0.00502
(1.00) 		0.0606
(1.00) 		0.147
(1.00) 		0.0834
(1.00) 		0.187
(1.00) 		0.73
(1.00) 		0.00184
(1.00) 		0.669
(1.00) 		0.155
(1.00)
8p loss 40 (27%) 110 0.292
(1.00) 		0.546
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.14
(1.00) 		0.321
(1.00) 		0.884
(1.00) 		0.823
(1.00)
8q loss 11 (7%) 139 0.123
(1.00) 		0.599
(1.00) 		0.349
(1.00) 		0.661
(1.00) 		0.0572
(1.00) 		0.922
(1.00) 		0.0876
(1.00) 		0.584
(1.00)
9p loss 30 (20%) 120 0.0712
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.572
(1.00) 		0.885
(1.00) 		0.717
(1.00) 		0.589
(1.00) 		0.972
(1.00) 		0.519
(1.00)
9q loss 23 (15%) 127 0.0548
(1.00) 		0.0471
(1.00) 		0.756
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.621
(1.00)
10p loss 30 (20%) 120 0.0761
(1.00) 		0.262
(1.00) 		0.0988
(1.00) 		0.0159
(1.00) 		0.0997
(1.00) 		0.895
(1.00) 		0.0511
(1.00) 		0.537
(1.00) 		0.104
(1.00)
10q loss 33 (22%) 117 0.0123
(1.00) 		0.0553
(1.00) 		0.205
(1.00) 		0.0036
(1.00) 		0.0558
(1.00) 		0.856
(1.00) 		0.109
(1.00) 		0.257
(1.00) 		0.0953
(1.00)
11p loss 47 (31%) 103 0.974
(1.00) 		0.0941
(1.00) 		0.824
(1.00) 		0.825
(1.00) 		0.543
(1.00) 		0.0773
(1.00) 		0.815
(1.00) 		0.605
(1.00) 		0.435
(1.00)
11q loss 60 (40%) 90 0.827
(1.00) 		0.00449
(1.00) 		0.671
(1.00) 		1
(1.00) 		1
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.994
(1.00) 		0.257
(1.00)
12p loss 22 (15%) 128 0.529
(1.00) 		0.672
(1.00) 		0.55
(1.00) 		1
(1.00) 		1
(1.00) 		0.853
(1.00) 		0.764
(1.00) 		0.831
(1.00) 		0.675
(1.00)
12q loss 7 (5%) 143 0.576
(1.00) 		0.106
(1.00) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.989
(1.00) 		0.0909
(1.00)
13q loss 39 (26%) 111 0.481
(1.00) 		0.208
(1.00) 		0.141
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.0641
(1.00) 		0.461
(1.00) 		0.114
(1.00) 		0.32
(1.00)
14q loss 17 (11%) 133 0.921
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.308
(1.00) 		0.203
(1.00)
15q loss 20 (13%) 130 0.873
(1.00) 		0.345
(1.00) 		0.759
(1.00) 		0.769
(1.00) 		0.352
(1.00) 		0.526
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.52
(1.00)
16p loss 16 (11%) 134 0.386
(1.00) 		0.141
(1.00) 		0.504
(1.00) 		0.33
(1.00) 		0.051
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.0241
(1.00) 		0.623
(1.00)
17p loss 47 (31%) 103 0.301
(1.00) 		0.155
(1.00) 		1
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.125
(1.00) 		0.639
(1.00) 		0.473
(1.00) 		0.553
(1.00)
17q loss 16 (11%) 134 0.133
(1.00) 		0.0334
(1.00) 		0.726
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.732
(1.00) 		0.759
(1.00) 		0.00332
(1.00)
18p loss 28 (19%) 122 0.642
(1.00) 		0.465
(1.00) 		0.0923
(1.00) 		0.171
(1.00) 		0.778
(1.00) 		0.583
(1.00) 		0.258
(1.00) 		0.761
(1.00) 		0.0359
(1.00)
18q loss 38 (25%) 112 0.399
(1.00) 		0.89
(1.00) 		0.449
(1.00) 		0.0249
(1.00) 		0.45
(1.00) 		0.057
(1.00) 		0.802
(1.00) 		0.756
(1.00) 		0.723
(1.00)
19p loss 25 (17%) 125 0.127
(1.00) 		0.821
(1.00) 		0.754
(1.00) 		0.0325
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.375
(1.00) 		0.602
(1.00) 		0.851
(1.00)
19q loss 12 (8%) 138 0.778
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.789
(1.00) 		0.627
(1.00) 		0.116
(1.00) 		0.629
(1.00)
20p loss 10 (7%) 140 0.709
(1.00) 		0.143
(1.00) 		1
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.901
(1.00) 		0.215
(1.00) 		0.0196
(1.00) 		0.0278
(1.00)
20q loss 4 (3%) 146 0.226
(1.00) 		0.0833
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.955
(1.00) 		1
(1.00) 		0.85
(1.00)
21q loss 20 (13%) 130 0.223
(1.00) 		0.913
(1.00) 		0.382
(1.00) 		0.775
(1.00) 		0.352
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.417
(1.00)
22q loss 30 (20%) 120 0.325
(1.00) 		0.4
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.108
(1.00) 		0.809
(1.00) 		0.534
(1.00)
xq loss 31 (21%) 119 0.0693
(1.00) 		0.882
(1.00) 		0.449
(1.00) 		0.807
(1.00) 		0.651
(1.00) 		0.541
(1.00) 		0.601
(1.00) 		0.989
(1.00) 		0.638
(1.00)
'2p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.9e-05 (t-test), Q value = 0.02

Table S1.  Gene #43: '2p loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 93 1.1 (2.3)
2P LOSS MUTATED 4 0.0 (0.0)
2P LOSS WILD-TYPE 89 1.1 (2.4)

Figure S1.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000101 (Chi-square test), Q value = 0.069

Table S2.  Gene #69: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE ENDOCERVICAL TYPE OF ADENOCARCINOMA ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
ALL 2 124 4 16 1 3
16Q LOSS MUTATED 0 11 2 7 1 0
16Q LOSS WILD-TYPE 2 113 2 9 0 3

Figure S2.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

  • Clinical data file = CESC-TP.merged_data.txt

  • Number of patients = 150

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 9

  • 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

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

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] 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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