Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1TD9W6H
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/C1TD9W6H
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 70 arm-level events and 11 clinical features across 221 patients, 41 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death'.

  • 1q gain cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 17p gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 3q loss cnv correlated to 'Time to Death'.

  • 4p loss cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.T.STAGE', and 'GENDER'.

  • 4q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 5p loss cnv correlated to 'Time to Death'.

  • 5q loss cnv correlated to 'Time to Death'.

  • 8p loss cnv correlated to 'Time to Death'.

  • 9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 11p loss cnv correlated to 'Time to Death'.

  • 11q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 13q loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.T.STAGE', and 'GENDER'.

  • 16q loss cnv correlated to 'Time to Death'.

  • 18p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 18q loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 19p loss cnv correlated to 'Time to Death'.

  • 19q loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 22q loss cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.T.STAGE', and 'GENDER'.

  • xq loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 41 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
13q loss 21 (10%) 200 0.000166
(0.112) 		0.011
(1.00) 		0.00031
(0.206) 		9e-05
(0.0607) 		0.00209
(1.00) 		0.524
(1.00) 		0.000149
(0.1) 		0.279
(1.00) 		0.205
(1.00) 		0.591
(1.00)
1q gain 15 (7%) 206 4e-08
(2.81e-05) 		0.755
(1.00) 		3e-05
(0.0203) 		2e-05
(0.0137) 		0.112
(1.00) 		0.154
(1.00) 		0.137
(1.00) 		0.0483
(1.00) 		0.0901
(1.00) 		1
(1.00)
4p loss 20 (9%) 201 0.0651
(1.00) 		0.00888
(1.00) 		1e-05
(0.00696) 		1e-05
(0.00696) 		0.00107
(0.7) 		0.843
(1.00) 		6.4e-05
(0.0433) 		0.181
(1.00) 		1
(1.00) 		0.101
(1.00) 		0.518
(1.00)
18q loss 36 (16%) 185 1.06e-06
(0.00074) 		0.411
(1.00) 		1e-05
(0.00696) 		1e-05
(0.00696) 		0.0137
(1.00) 		0.0396
(1.00) 		0.0694
(1.00) 		0.288
(1.00) 		0.66
(1.00) 		0.093
(1.00) 		1
(1.00)
19q loss 12 (5%) 209 1.26e-12
(8.86e-10) 		0.972
(1.00) 		0.00013
(0.0876) 		0.0002
(0.134) 		0.0584
(1.00) 		0.102
(1.00) 		0.105
(1.00) 		0.12
(1.00) 		0.496
(1.00) 		0.685
(1.00) 		1
(1.00)
22q loss 50 (23%) 171 0.00165
(1.00) 		0.112
(1.00) 		1e-05
(0.00696) 		1e-05
(0.00696) 		0.0119
(1.00) 		0.0329
(1.00) 		0.000289
(0.193) 		0.297
(1.00) 		0.477
(1.00) 		0.201
(1.00) 		0.395
(1.00)
xq loss 21 (10%) 200 1.84e-06
(0.00128) 		0.135
(1.00) 		0.00017
(0.114) 		1e-05
(0.00696) 		0.0351
(1.00) 		0.254
(1.00) 		0.0717
(1.00) 		0.27
(1.00) 		0.496
(1.00) 		0.0132
(1.00) 		1
(1.00)
4q loss 21 (10%) 200 0.133
(1.00) 		0.0578
(1.00) 		2e-05
(0.0137) 		5e-05
(0.0338) 		0.00577
(1.00) 		0.321
(1.00) 		0.0014
(0.911) 		0.12
(1.00) 		0.532
(1.00) 		0.149
(1.00) 		0.543
(1.00)
9p loss 26 (12%) 195 0.0163
(1.00) 		0.511
(1.00) 		1e-05
(0.00696) 		1e-05
(0.00696) 		0.0181
(1.00) 		0.0744
(1.00) 		0.00455
(1.00) 		0.00717
(1.00) 		0.0234
(1.00) 		0.0422
(1.00) 		0.602
(1.00)
9q loss 27 (12%) 194 0.00337
(1.00) 		0.454
(1.00) 		1e-05
(0.00696) 		2e-05
(0.0137) 		0.0179
(1.00) 		0.406
(1.00) 		0.00627
(1.00) 		0.0177
(1.00) 		0.213
(1.00) 		0.101
(1.00) 		0.601
(1.00)
11q loss 16 (7%) 205 0.00351
(1.00) 		0.245
(1.00) 		1e-05
(0.00696) 		1e-05
(0.00696) 		0.0522
(1.00) 		0.0972
(1.00) 		0.401
(1.00) 		0.275
(1.00) 		0.882
(1.00) 		0.116
(1.00) 		1
(1.00)
18p loss 33 (15%) 188 0.0019
(1.00) 		0.116
(1.00) 		2e-05
(0.0137) 		1e-05
(0.00696) 		0.0176
(1.00) 		0.0216
(1.00) 		0.0347
(1.00) 		0.4
(1.00) 		0.45
(1.00) 		0.428
(1.00) 		1
(1.00)
1p gain 8 (4%) 213 1.5e-14
(1.06e-11) 		0.438
(1.00) 		0.00154
(0.999) 		0.00763
(1.00) 		0.00662
(1.00) 		0.0824
(1.00) 		0.044
(1.00) 		0.37
(1.00) 		1
(1.00)
17p gain 135 (61%) 86 0.53
(1.00) 		0.00319
(1.00) 		0.0005
(0.33) 		0.00383
(1.00) 		0.771
(1.00) 		0.00021
(0.14) 		0.126
(1.00) 		0.715
(1.00) 		0.606
(1.00) 		0.411
(1.00) 		0.28
(1.00)
3q loss 5 (2%) 216 3.26e-12
(2.29e-09) 		0.149
(1.00) 		0.0171
(1.00) 		0.0204
(1.00) 		0.0822
(1.00) 		0.172
(1.00) 		0.625
(1.00) 		1
(1.00) 		1
(1.00)
5p loss 8 (4%) 213 1.06e-06
(0.00074) 		0.072
(1.00) 		0.0263
(1.00) 		0.00804
(1.00) 		0.0178
(1.00) 		0.21
(1.00) 		0.044
(1.00) 		0.748
(1.00) 		0.263
(1.00)
5q loss 8 (4%) 213 2.47e-05
(0.0167) 		0.0166
(1.00) 		0.0472
(1.00) 		0.0079
(1.00) 		0.0338
(1.00) 		0.21
(1.00) 		0.044
(1.00) 		0.749
(1.00) 		0.263
(1.00)
8p loss 11 (5%) 210 0.000328
(0.218) 		0.283
(1.00) 		0.0451
(1.00) 		0.497
(1.00) 		0.00405
(1.00) 		0.00795
(1.00) 		0.301
(1.00) 		0.484
(1.00) 		0.0357
(1.00) 		1
(1.00)
11p loss 14 (6%) 207 3e-07
(0.00021) 		0.0838
(1.00) 		0.0109
(1.00) 		0.00389
(1.00) 		0.0586
(1.00) 		0.413
(1.00) 		0.548
(1.00) 		0.19
(1.00) 		0.678
(1.00) 		1
(1.00) 		1
(1.00)
16q loss 6 (3%) 215 1.05e-07
(7.33e-05) 		0.202
(1.00) 		0.0179
(1.00) 		0.0469
(1.00) 		0.0843
(1.00) 		0.761
(1.00) 		0.356
(1.00) 		0.633
(1.00) 		1
(1.00)
19p loss 13 (6%) 208 0.000199
(0.133) 		0.172
(1.00) 		0.00567
(1.00) 		0.00359
(1.00) 		0.0588
(1.00) 		0.189
(1.00) 		0.526
(1.00) 		0.12
(1.00) 		0.419
(1.00) 		1
(1.00) 		1
(1.00)
2p gain 38 (17%) 183 0.791
(1.00) 		0.235
(1.00) 		0.0746
(1.00) 		0.551
(1.00) 		0.104
(1.00) 		0.00301
(1.00) 		0.694
(1.00) 		0.606
(1.00) 		0.364
(1.00) 		0.74
(1.00) 		0.673
(1.00)
2q gain 41 (19%) 180 0.747
(1.00) 		0.421
(1.00) 		0.0213
(1.00) 		0.66
(1.00) 		0.0778
(1.00) 		0.00847
(1.00) 		0.702
(1.00) 		0.463
(1.00) 		0.364
(1.00) 		0.673
(1.00) 		1
(1.00)
3p gain 62 (28%) 159 0.12
(1.00) 		0.923
(1.00) 		0.0223
(1.00) 		0.00809
(1.00) 		0.844
(1.00) 		0.213
(1.00) 		0.411
(1.00) 		0.0189
(1.00) 		0.247
(1.00) 		0.492
(1.00) 		1
(1.00)
3q gain 73 (33%) 148 0.254
(1.00) 		0.621
(1.00) 		0.184
(1.00) 		0.0615
(1.00) 		0.886
(1.00) 		0.136
(1.00) 		0.269
(1.00) 		0.161
(1.00) 		0.518
(1.00) 		0.193
(1.00) 		0.72
(1.00)
4p gain 9 (4%) 212 0.0425
(1.00) 		0.0366
(1.00) 		0.0637
(1.00) 		0.398
(1.00) 		0.32
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.324
(1.00) 		0.601
(1.00) 		1
(1.00)
4q gain 8 (4%) 213 0.0425
(1.00) 		0.0974
(1.00) 		0.242
(1.00) 		0.35
(1.00) 		0.131
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.762
(1.00) 		1
(1.00)
5p gain 29 (13%) 192 0.979
(1.00) 		0.508
(1.00) 		0.261
(1.00) 		0.176
(1.00) 		0.468
(1.00) 		0.372
(1.00) 		0.664
(1.00) 		0.154
(1.00) 		0.868
(1.00) 		0.484
(1.00) 		0.605
(1.00)
5q gain 29 (13%) 192 0.979
(1.00) 		0.865
(1.00) 		0.26
(1.00) 		0.267
(1.00) 		0.88
(1.00) 		0.373
(1.00) 		0.664
(1.00) 		0.154
(1.00) 		0.868
(1.00) 		0.644
(1.00) 		0.608
(1.00)
6p gain 8 (4%) 213 0.595
(1.00) 		0.405
(1.00) 		0.00164
(1.00) 		0.00063
(0.415) 		0.217
(1.00) 		0.0351
(1.00) 		0.691
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
6q gain 6 (3%) 215 0.815
(1.00) 		0.127
(1.00) 		0.0103
(1.00) 		0.00648
(1.00) 		0.0559
(1.00) 		0.0198
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.718
(1.00) 		1
(1.00)
7p gain 130 (59%) 91 0.435
(1.00) 		0.077
(1.00) 		0.00141
(0.916) 		0.0307
(1.00) 		0.704
(1.00) 		0.681
(1.00) 		0.0353
(1.00) 		0.0595
(1.00) 		0.678
(1.00) 		0.824
(1.00) 		0.487
(1.00)
7q gain 131 (59%) 90 0.422
(1.00) 		0.056
(1.00) 		0.00087
(0.572) 		0.025
(1.00) 		0.711
(1.00) 		0.795
(1.00) 		0.0335
(1.00) 		0.0595
(1.00) 		0.678
(1.00) 		0.794
(1.00) 		0.316
(1.00)
8p gain 14 (6%) 207 0.118
(1.00) 		0.898
(1.00) 		0.17
(1.00) 		0.106
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.107
(1.00) 		0.0911
(1.00) 		1
(1.00)
8q gain 18 (8%) 203 0.118
(1.00) 		0.474
(1.00) 		0.00092
(0.604) 		0.00043
(0.285) 		0.00345
(1.00) 		0.202
(1.00) 		0.0533
(1.00) 		0.434
(1.00) 		0.882
(1.00) 		0.089
(1.00) 		1
(1.00)
9p gain 3 (1%) 218 0.491
(1.00) 		0.046
(1.00) 		0.0354
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.611
(1.00) 		1
(1.00)
10p gain 8 (4%) 213 0.745
(1.00) 		0.342
(1.00) 		0.262
(1.00) 		0.421
(1.00) 		1
(1.00) 		0.0317
(1.00) 		0.691
(1.00) 		0.00629
(1.00) 		1
(1.00)
10q gain 8 (4%) 213 0.745
(1.00) 		0.342
(1.00) 		0.265
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.033
(1.00) 		0.691
(1.00) 		0.00589
(1.00) 		1
(1.00)
11p gain 10 (5%) 211 0.527
(1.00) 		0.105
(1.00) 		0.114
(1.00) 		0.153
(1.00) 		0.517
(1.00) 		0.0358
(1.00) 		0.153
(1.00) 		0.241
(1.00) 		1
(1.00)
11q gain 10 (5%) 211 0.513
(1.00) 		0.0896
(1.00) 		0.181
(1.00) 		0.148
(1.00) 		0.693
(1.00) 		0.22
(1.00) 		0.0338
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.39
(1.00) 		1
(1.00)
12p gain 91 (41%) 130 0.0678
(1.00) 		0.561
(1.00) 		0.14
(1.00) 		0.909
(1.00) 		0.575
(1.00) 		0.214
(1.00) 		0.00974
(1.00) 		0.415
(1.00) 		0.973
(1.00) 		0.868
(1.00) 		0.0802
(1.00)
12q gain 91 (41%) 130 0.0678
(1.00) 		0.561
(1.00) 		0.139
(1.00) 		0.91
(1.00) 		0.575
(1.00) 		0.217
(1.00) 		0.00974
(1.00) 		0.415
(1.00) 		0.973
(1.00) 		0.868
(1.00) 		0.0802
(1.00)
13q gain 23 (10%) 198 0.804
(1.00) 		0.408
(1.00) 		0.404
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.811
(1.00) 		0.38
(1.00) 		0.755
(1.00) 		0.254
(1.00)
14q gain 3 (1%) 218 0.036
(1.00) 		0.0201
(1.00) 		0.629
(1.00) 		0.196
(1.00) 		1
(1.00)
15q gain 5 (2%) 216 0.6
(1.00) 		1
(1.00) 		0.279
(1.00) 		0.238
(1.00) 		0.498
(1.00) 		0.141
(1.00) 		0.67
(1.00) 		1
(1.00)
16p gain 117 (53%) 104 0.2
(1.00) 		0.175
(1.00) 		0.933
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.00702
(1.00) 		0.681
(1.00) 		0.651
(1.00) 		0.0138
(1.00) 		0.0848
(1.00)
16q gain 113 (51%) 108 0.0463
(1.00) 		0.347
(1.00) 		0.758
(1.00) 		0.372
(1.00) 		0.65
(1.00) 		0.209
(1.00) 		0.0372
(1.00) 		0.246
(1.00) 		0.96
(1.00) 		0.0725
(1.00) 		0.0917
(1.00)
17q gain 149 (67%) 72 0.245
(1.00) 		0.0128
(1.00) 		0.0576
(1.00) 		0.189
(1.00) 		0.453
(1.00) 		0.00545
(1.00) 		0.432
(1.00) 		0.853
(1.00) 		0.71
(1.00) 		0.411
(1.00) 		0.452
(1.00)
18p gain 11 (5%) 210 0.188
(1.00) 		0.783
(1.00) 		0.179
(1.00) 		0.563
(1.00) 		0.392
(1.00) 		0.319
(1.00) 		0.186
(1.00) 		0.66
(1.00) 		0.79
(1.00) 		0.204
(1.00) 		1
(1.00)
18q gain 8 (4%) 213 0.623
(1.00) 		0.624
(1.00) 		0.509
(1.00) 		0.348
(1.00) 		0.777
(1.00) 		0.445
(1.00) 		0.176
(1.00) 		0.332
(1.00) 		1
(1.00)
19p gain 4 (2%) 217 0.768
(1.00) 		0.245
(1.00) 		0.584
(1.00) 		0.529
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.631
(1.00) 		1
(1.00)
19q gain 4 (2%) 217 0.768
(1.00) 		0.245
(1.00) 		0.583
(1.00) 		0.526
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00)
20p gain 74 (33%) 147 0.827
(1.00) 		0.105
(1.00) 		0.699
(1.00) 		0.323
(1.00) 		0.897
(1.00) 		0.935
(1.00) 		0.636
(1.00) 		0.495
(1.00) 		0.752
(1.00) 		0.592
(1.00) 		0.72
(1.00)
20q gain 76 (34%) 145 0.847
(1.00) 		0.096
(1.00) 		0.561
(1.00) 		0.247
(1.00) 		0.805
(1.00) 		0.87
(1.00) 		0.531
(1.00) 		0.495
(1.00) 		0.752
(1.00) 		0.551
(1.00) 		0.721
(1.00)
21q gain 15 (7%) 206 0.623
(1.00) 		0.0566
(1.00) 		0.956
(1.00) 		0.838
(1.00) 		0.693
(1.00) 		0.171
(1.00) 		0.768
(1.00) 		0.751
(1.00) 		0.115
(1.00) 		0.518
(1.00)
22q gain 3 (1%) 218 0.322
(1.00) 		0.272
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.56
(1.00) 		0.612
(1.00) 		0.14
(1.00)
xq gain 70 (32%) 151 0.338
(1.00) 		0.98
(1.00) 		0.0186
(1.00) 		0.0391
(1.00) 		0.673
(1.00) 		0.963
(1.00) 		0.0775
(1.00) 		0.0219
(1.00) 		0.861
(1.00) 		0.23
(1.00) 		0.721
(1.00)
1p loss 21 (10%) 200 0.87
(1.00) 		0.532
(1.00) 		0.186
(1.00) 		0.199
(1.00) 		0.695
(1.00) 		0.509
(1.00) 		0.316
(1.00) 		0.861
(1.00) 		0.366
(1.00) 		0.543
(1.00)
1q loss 16 (7%) 205 0.484
(1.00) 		0.474
(1.00) 		0.555
(1.00) 		0.777
(1.00) 		0.693
(1.00) 		0.534
(1.00) 		0.163
(1.00) 		0.861
(1.00) 		0.459
(1.00) 		0.543
(1.00)
3p loss 17 (8%) 204 0.000506
(0.334) 		0.137
(1.00) 		0.0004
(0.266) 		0.00117
(0.764) 		0.491
(1.00) 		0.0827
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.982
(1.00) 		0.454
(1.00) 		1
(1.00)
6p loss 16 (7%) 205 0.123
(1.00) 		0.275
(1.00) 		0.0234
(1.00) 		0.0459
(1.00) 		0.0479
(1.00) 		0.777
(1.00) 		0.163
(1.00) 		0.934
(1.00) 		0.0459
(1.00) 		1
(1.00)
6q loss 19 (9%) 202 0.625
(1.00) 		0.945
(1.00) 		0.0312
(1.00) 		0.00133
(0.867) 		0.064
(1.00) 		0.307
(1.00) 		0.0298
(1.00) 		0.279
(1.00) 		0.677
(1.00) 		0.0319
(1.00) 		1
(1.00)
8q loss 6 (3%) 215 0.000462
(0.306) 		0.95
(1.00) 		0.243
(1.00) 		0.655
(1.00) 		0.285
(1.00) 		0.356
(1.00) 		0.224
(1.00) 		1
(1.00)
10p loss 13 (6%) 208 0.00697
(1.00) 		0.925
(1.00) 		0.00199
(1.00) 		0.00382
(1.00) 		0.0352
(1.00) 		0.0372
(1.00) 		0.202
(1.00) 		0.139
(1.00) 		0.84
(1.00) 		1
(1.00)
10q loss 13 (6%) 208 0.00451
(1.00) 		0.349
(1.00) 		0.00078
(0.513) 		0.00104
(0.681) 		0.0133
(1.00) 		0.13
(1.00) 		0.202
(1.00) 		0.0415
(1.00) 		0.493
(1.00) 		1
(1.00)
14q loss 39 (18%) 182 0.00653
(1.00) 		0.835
(1.00) 		0.0055
(1.00) 		0.00447
(1.00) 		0.0221
(1.00) 		0.153
(1.00) 		0.0106
(1.00) 		0.0445
(1.00) 		0.0822
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 24 (11%) 197 0.00205
(1.00) 		0.0781
(1.00) 		0.00326
(1.00) 		0.00187
(1.00) 		0.0354
(1.00) 		0.326
(1.00) 		0.34
(1.00) 		0.125
(1.00) 		0.443
(1.00) 		1
(1.00)
16p loss 4 (2%) 217 0.748
(1.00) 		0.0943
(1.00) 		0.0902
(1.00) 		1
(1.00) 		0.071
(1.00) 		1
(1.00)
17p loss 7 (3%) 214 0.72
(1.00) 		0.84
(1.00) 		0.00172
(1.00) 		0.00774
(1.00) 		0.0336
(1.00) 		0.0344
(1.00) 		0.104
(1.00) 		0.324
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 33 (15%) 188 0.302
(1.00) 		0.417
(1.00) 		0.0117
(1.00) 		0.00446
(1.00) 		0.651
(1.00) 		0.175
(1.00) 		0.0347
(1.00) 		0.0791
(1.00) 		0.735
(1.00) 		0.573
(1.00) 		1
(1.00)
'1p gain' versus 'Time to Death'

P value = 1.5e-14 (logrank test), Q value = 1.1e-11

Table S1.  Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
1P GAIN MUTATED 6 2 26.0 - 579.0 (99.5)
1P GAIN WILD-TYPE 188 5 2.0 - 5925.0 (550.0)

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'Time to Death'

P value = 4e-08 (logrank test), Q value = 2.8e-05

Table S2.  Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
1Q GAIN MUTATED 12 3 21.0 - 1967.0 (160.0)
1Q GAIN WILD-TYPE 182 4 2.0 - 5925.0 (550.0)

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S3.  Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
1Q GAIN MUTATED 2 0 10 3
1Q GAIN WILD-TYPE 135 16 33 10

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1q gain' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S4.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
1Q GAIN MUTATED 3 0 12
1Q GAIN WILD-TYPE 143 22 39

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'17p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S5.  Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 88 8 112
17P GAIN MUTATED 42 2 81
17P GAIN WILD-TYPE 46 6 31

Figure S5.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'3q loss' versus 'Time to Death'

P value = 3.26e-12 (logrank test), Q value = 2.3e-09

Table S6.  Gene #43: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
3Q LOSS MUTATED 4 2 112.0 - 270.0 (235.0)
3Q LOSS WILD-TYPE 190 5 2.0 - 5925.0 (550.0)

Figure S6.  Get High-res Image Gene #43: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S7.  Gene #44: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
4P LOSS MUTATED 3 1 14 1
4P LOSS WILD-TYPE 134 15 29 12

Figure S7.  Get High-res Image Gene #44: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S8.  Gene #44: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
4P LOSS MUTATED 4 2 14
4P LOSS WILD-TYPE 142 20 37

Figure S8.  Get High-res Image Gene #44: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'GENDER'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.043

Table S9.  Gene #44: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 63 158
4P LOSS MUTATED 14 6
4P LOSS WILD-TYPE 49 152

Figure S9.  Get High-res Image Gene #44: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S10.  Gene #45: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
4Q LOSS MUTATED 4 1 13 2
4Q LOSS WILD-TYPE 133 15 30 11

Figure S10.  Get High-res Image Gene #45: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4q loss' versus 'PATHOLOGY.T.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.034

Table S11.  Gene #45: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
4Q LOSS MUTATED 5 3 13
4Q LOSS WILD-TYPE 141 19 38

Figure S11.  Get High-res Image Gene #45: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'Time to Death'

P value = 1.06e-06 (logrank test), Q value = 0.00074

Table S12.  Gene #46: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
5P LOSS MUTATED 5 1 2.0 - 554.0 (84.0)
5P LOSS WILD-TYPE 189 6 2.0 - 5925.0 (546.0)

Figure S12.  Get High-res Image Gene #46: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'Time to Death'

P value = 2.47e-05 (logrank test), Q value = 0.017

Table S13.  Gene #47: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
5Q LOSS MUTATED 6 1 2.0 - 554.0 (90.5)
5Q LOSS WILD-TYPE 188 6 2.0 - 5925.0 (562.0)

Figure S13.  Get High-res Image Gene #47: '5q loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'Time to Death'

P value = 0.000328 (logrank test), Q value = 0.22

Table S14.  Gene #50: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
8P LOSS MUTATED 9 2 10.0 - 1967.0 (262.0)
8P LOSS WILD-TYPE 185 5 2.0 - 5925.0 (554.0)

Figure S14.  Get High-res Image Gene #50: '8p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S15.  Gene #52: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
9P LOSS MUTATED 6 0 13 5
9P LOSS WILD-TYPE 131 16 30 8

Figure S15.  Get High-res Image Gene #52: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S16.  Gene #52: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
9P LOSS MUTATED 7 2 17
9P LOSS WILD-TYPE 139 20 34

Figure S16.  Get High-res Image Gene #52: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S17.  Gene #53: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
9Q LOSS MUTATED 7 1 14 4
9Q LOSS WILD-TYPE 130 15 29 9

Figure S17.  Get High-res Image Gene #53: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S18.  Gene #53: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
9Q LOSS MUTATED 8 1 18
9Q LOSS WILD-TYPE 138 21 33

Figure S18.  Get High-res Image Gene #53: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'11p loss' versus 'Time to Death'

P value = 3e-07 (logrank test), Q value = 0.00021

Table S19.  Gene #56: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
11P LOSS MUTATED 12 3 21.0 - 1967.0 (215.5)
11P LOSS WILD-TYPE 182 4 2.0 - 5925.0 (550.0)

Figure S19.  Get High-res Image Gene #56: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S20.  Gene #57: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
11Q LOSS MUTATED 2 1 9 4
11Q LOSS WILD-TYPE 135 15 34 9

Figure S20.  Get High-res Image Gene #57: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S21.  Gene #57: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
11Q LOSS MUTATED 2 1 13
11Q LOSS WILD-TYPE 144 21 38

Figure S21.  Get High-res Image Gene #57: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'Time to Death'

P value = 0.000166 (logrank test), Q value = 0.11

Table S22.  Gene #58: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
13Q LOSS MUTATED 17 3 4.0 - 2639.0 (112.0)
13Q LOSS WILD-TYPE 177 4 2.0 - 5925.0 (579.0)

Figure S22.  Get High-res Image Gene #58: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #58: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
13Q LOSS MUTATED 6 1 11 3
13Q LOSS WILD-TYPE 131 15 32 10

Figure S23.  Get High-res Image Gene #58: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'PATHOLOGY.T.STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.061

Table S24.  Gene #58: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
13Q LOSS MUTATED 6 2 13
13Q LOSS WILD-TYPE 140 20 38

Figure S24.  Get High-res Image Gene #58: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'GENDER'

P value = 0.000149 (Fisher's exact test), Q value = 0.1

Table S25.  Gene #58: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 63 158
13Q LOSS MUTATED 14 7
13Q LOSS WILD-TYPE 49 151

Figure S25.  Get High-res Image Gene #58: '13q loss' versus Clinical Feature #7: 'GENDER'

'16q loss' versus 'Time to Death'

P value = 1.05e-07 (logrank test), Q value = 7.3e-05

Table S26.  Gene #62: '16q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
16Q LOSS MUTATED 3 2 21.0 - 1967.0 (87.0)
16Q LOSS WILD-TYPE 191 5 2.0 - 5925.0 (541.0)

Figure S26.  Get High-res Image Gene #62: '16q loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S27.  Gene #64: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
18P LOSS MUTATED 10 1 15 5
18P LOSS WILD-TYPE 127 15 28 8

Figure S27.  Get High-res Image Gene #64: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S28.  Gene #64: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
18P LOSS MUTATED 10 3 20
18P LOSS WILD-TYPE 136 19 31

Figure S28.  Get High-res Image Gene #64: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'18q loss' versus 'Time to Death'

P value = 1.06e-06 (logrank test), Q value = 0.00074

Table S29.  Gene #65: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
18Q LOSS MUTATED 31 6 4.0 - 3760.0 (232.0)
18Q LOSS WILD-TYPE 163 1 2.0 - 5925.0 (579.0)

Figure S29.  Get High-res Image Gene #65: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S30.  Gene #65: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
18Q LOSS MUTATED 10 1 18 5
18Q LOSS WILD-TYPE 127 15 25 8

Figure S30.  Get High-res Image Gene #65: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S31.  Gene #65: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
18Q LOSS MUTATED 11 3 22
18Q LOSS WILD-TYPE 135 19 29

Figure S31.  Get High-res Image Gene #65: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'19p loss' versus 'Time to Death'

P value = 0.000199 (logrank test), Q value = 0.13

Table S32.  Gene #66: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
19P LOSS MUTATED 13 3 29.0 - 2584.0 (428.0)
19P LOSS WILD-TYPE 181 4 2.0 - 5925.0 (541.0)

Figure S32.  Get High-res Image Gene #66: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'Time to Death'

P value = 1.26e-12 (logrank test), Q value = 8.9e-10

Table S33.  Gene #67: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
19Q LOSS MUTATED 12 4 29.0 - 1967.0 (215.5)
19Q LOSS WILD-TYPE 182 3 2.0 - 5925.0 (562.0)

Figure S33.  Get High-res Image Gene #67: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.088

Table S34.  Gene #67: '19q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
19Q LOSS MUTATED 1 1 8 1
19Q LOSS WILD-TYPE 136 15 35 12

Figure S34.  Get High-res Image Gene #67: '19q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'19q loss' versus 'PATHOLOGY.T.STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #67: '19q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
19Q LOSS MUTATED 2 1 9
19Q LOSS WILD-TYPE 144 21 42

Figure S35.  Get High-res Image Gene #67: '19q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'22q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S36.  Gene #69: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
22Q LOSS MUTATED 17 3 21 7
22Q LOSS WILD-TYPE 120 13 22 6

Figure S36.  Get High-res Image Gene #69: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'22q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S37.  Gene #69: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
22Q LOSS MUTATED 20 3 27
22Q LOSS WILD-TYPE 126 19 24

Figure S37.  Get High-res Image Gene #69: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'22q loss' versus 'GENDER'

P value = 0.000289 (Fisher's exact test), Q value = 0.19

Table S38.  Gene #69: '22q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 63 158
22Q LOSS MUTATED 25 25
22Q LOSS WILD-TYPE 38 133

Figure S38.  Get High-res Image Gene #69: '22q loss' versus Clinical Feature #7: 'GENDER'

'xq loss' versus 'Time to Death'

P value = 1.84e-06 (logrank test), Q value = 0.0013

Table S39.  Gene #70: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
XQ LOSS MUTATED 17 4 4.0 - 2429.0 (307.0)
XQ LOSS WILD-TYPE 177 3 2.0 - 5925.0 (579.0)

Figure S39.  Get High-res Image Gene #70: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #70: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
XQ LOSS MUTATED 5 1 11 3
XQ LOSS WILD-TYPE 132 15 32 10

Figure S40.  Get High-res Image Gene #70: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'xq loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S41.  Gene #70: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
XQ LOSS MUTATED 6 1 14
XQ LOSS WILD-TYPE 140 21 37

Figure S41.  Get High-res Image Gene #70: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 221

  • Number of significantly arm-level cnvs = 70

  • Number of selected clinical features = 11

  • 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

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] 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)
[3] 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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