Correlation between copy number variations of arm-level result and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C13X84X3
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/C13X84X3
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 12 clinical features across 583 patients, 19 significant findings detected with Q value < 0.25.

  • 6Q GAIN MUTATION ANALYSIS cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • 7P GAIN MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • 13Q GAIN MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 14Q GAIN MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 20P GAIN MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20Q GAIN MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • 7P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 7Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 14Q LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 17P LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18P LOSS MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • 18Q LOSS MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • 22Q LOSS MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

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 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 19 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		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 Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test
18Q LOSS MUTATION ANALYSIS 385 (66%) 198 0.755
(1.00) 		0.116
(1.00) 		1.47e-08
(1.4e-05) 		6.91e-05
(0.0654) 		0.337
(1.00) 		0.00015
(0.142) 		0.000287
(0.27) 		0.599
(1.00) 		4.39e-16
(4.21e-13) 		0.285
(1.00) 		0.0245
(1.00) 		0.108
(1.00)
7P GAIN MUTATION ANALYSIS 333 (57%) 250 0.486
(1.00) 		0.39
(1.00) 		0.189
(1.00) 		0.00022
(0.207) 		0.843
(1.00) 		2.33e-05
(0.0221) 		0.0234
(1.00) 		0.737
(1.00) 		0.000624
(0.58) 		0.313
(1.00) 		0.259
(1.00) 		0.0146
(1.00)
20Q GAIN MUTATION ANALYSIS 441 (76%) 142 0.484
(1.00) 		0.417
(1.00) 		4.07e-06
(0.00386) 		0.000549
(0.51) 		0.224
(1.00) 		0.00378
(1.00) 		0.00276
(1.00) 		0.334
(1.00) 		2.23e-12
(2.14e-09) 		0.695
(1.00) 		0.0233
(1.00) 		0.35
(1.00)
18P LOSS MUTATION ANALYSIS 357 (61%) 226 0.741
(1.00) 		0.171
(1.00) 		1.59e-06
(0.00152) 		0.000337
(0.316) 		0.851
(1.00) 		0.0021
(1.00) 		0.000637
(0.591) 		0.496
(1.00) 		9.81e-16
(9.4e-13) 		0.164
(1.00) 		0.0236
(1.00) 		0.0987
(1.00)
6Q GAIN MUTATION ANALYSIS 105 (18%) 478 0.61
(1.00) 		0.723
(1.00) 		0.273
(1.00) 		0.105
(1.00) 		0.752
(1.00) 		0.00582
(1.00) 		0.17
(1.00) 		0.59
(1.00) 		0.0643
(1.00) 		0.000136
(0.128) 		0.333
(1.00) 		0.0955
(1.00)
13Q GAIN MUTATION ANALYSIS 349 (60%) 234 0.164
(1.00) 		0.238
(1.00) 		0.0578
(1.00) 		0.00822
(1.00) 		0.745
(1.00) 		0.00041
(0.382) 		0.0473
(1.00) 		0.272
(1.00) 		1.32e-08
(1.27e-05) 		0.747
(1.00) 		0.0876
(1.00) 		0.679
(1.00)
14Q GAIN MUTATION ANALYSIS 43 (7%) 540 0.599
(1.00) 		0.93
(1.00) 		0.377
(1.00) 		0.795
(1.00) 		0.926
(1.00) 		0.597
(1.00) 		0.000231
(0.218) 		0.634
(1.00) 		0.374
(1.00) 		0.137
(1.00) 		0.597
(1.00) 		0.22
(1.00)
20P GAIN MUTATION ANALYSIS 337 (58%) 246 0.237
(1.00) 		0.931
(1.00) 		0.00472
(1.00) 		0.000349
(0.327) 		0.699
(1.00) 		0.0339
(1.00) 		0.00188
(1.00) 		0.0649
(1.00) 		3e-06
(0.00286) 		0.315
(1.00) 		0.0428
(1.00) 		0.344
(1.00)
7P LOSS MUTATION ANALYSIS 4 (1%) 579 0.654
(1.00) 		0.257
(1.00) 		0.0651
(1.00) 		0.932
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.0533
(1.00) 		1
(1.00) 		1
(1.00) 		2.91e-25
(2.79e-22)
7Q LOSS MUTATION ANALYSIS 5 (1%) 578 0.545
(1.00) 		0.769
(1.00) 		0.13
(1.00) 		0.789
(1.00) 		0.422
(1.00) 		0.832
(1.00) 		0.82
(1.00) 		0.667
(1.00) 		0.0949
(1.00) 		1
(1.00) 		1
(1.00) 		2.17e-06
(0.00206)
14Q LOSS MUTATION ANALYSIS 187 (32%) 396 0.146
(1.00) 		0.646
(1.00) 		0.0282
(1.00) 		0.447
(1.00) 		0.464
(1.00) 		0.014
(1.00) 		0.102
(1.00) 		0.535
(1.00) 		1.98e-06
(0.00189) 		0.726
(1.00) 		0.906
(1.00) 		0.894
(1.00)
17P LOSS MUTATION ANALYSIS 319 (55%) 264 0.295
(1.00) 		0.141
(1.00) 		0.0198
(1.00) 		0.0092
(1.00) 		0.581
(1.00) 		0.00179
(1.00) 		0.0235
(1.00) 		0.279
(1.00) 		3.01e-06
(0.00286) 		0.194
(1.00) 		0.0726
(1.00) 		0.0069
(1.00)
22Q LOSS MUTATION ANALYSIS 186 (32%) 397 0.0689
(1.00) 		0.711
(1.00) 		0.619
(1.00) 		0.0109
(1.00) 		0.312
(1.00) 		2.93e-05
(0.0277) 		0.0217
(1.00) 		1
(1.00) 		0.024
(1.00) 		0.476
(1.00) 		0.601
(1.00) 		0.0216
(1.00)
1P GAIN MUTATION ANALYSIS 41 (7%) 542 0.889
(1.00) 		0.535
(1.00) 		0.855
(1.00) 		0.441
(1.00) 		0.801
(1.00) 		0.518
(1.00) 		0.643
(1.00) 		0.417
(1.00) 		0.0875
(1.00) 		0.484
(1.00) 		0.102
(1.00) 		0.133
(1.00)
1Q GAIN MUTATION ANALYSIS 111 (19%) 472 0.78
(1.00) 		0.436
(1.00) 		0.342
(1.00) 		0.14
(1.00) 		0.0754
(1.00) 		0.0652
(1.00) 		0.0643
(1.00) 		0.398
(1.00) 		0.269
(1.00) 		0.683
(1.00) 		0.265
(1.00) 		0.00578
(1.00)
2P GAIN MUTATION ANALYSIS 104 (18%) 479 0.652
(1.00) 		0.547
(1.00) 		0.278
(1.00) 		0.148
(1.00) 		0.419
(1.00) 		0.096
(1.00) 		0.407
(1.00) 		0.448
(1.00) 		0.0174
(1.00) 		0.666
(1.00) 		0.0366
(1.00) 		0.657
(1.00)
2Q GAIN MUTATION ANALYSIS 101 (17%) 482 0.265
(1.00) 		0.22
(1.00) 		0.141
(1.00) 		0.122
(1.00) 		0.501
(1.00) 		0.0405
(1.00) 		0.593
(1.00) 		0.381
(1.00) 		0.0123
(1.00) 		0.658
(1.00) 		0.384
(1.00) 		0.52
(1.00)
3P GAIN MUTATION ANALYSIS 65 (11%) 518 0.526
(1.00) 		0.14
(1.00) 		0.0368
(1.00) 		0.0272
(1.00) 		1
(1.00) 		0.219
(1.00) 		0.00121
(1.00) 		0.51
(1.00) 		0.0797
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.187
(1.00)
3Q GAIN MUTATION ANALYSIS 89 (15%) 494 0.113
(1.00) 		0.214
(1.00) 		0.0272
(1.00) 		0.0392
(1.00) 		0.902
(1.00) 		0.0359
(1.00) 		0.000301
(0.282) 		0.729
(1.00) 		0.0286
(1.00) 		0.633
(1.00) 		0.444
(1.00) 		0.163
(1.00)
4P GAIN MUTATION ANALYSIS 14 (2%) 569 0.761
(1.00) 		0.847
(1.00) 		0.0278
(1.00) 		0.412
(1.00) 		0.512
(1.00) 		0.494
(1.00) 		0.206
(1.00) 		0.589
(1.00) 		0.0719
(1.00) 		1
(1.00) 		1
(1.00) 		0.0202
(1.00)
4Q GAIN MUTATION ANALYSIS 15 (3%) 568 0.246
(1.00) 		0.475
(1.00) 		1
(1.00) 		0.93
(1.00) 		0.859
(1.00) 		0.362
(1.00) 		0.555
(1.00) 		0.794
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.623
(1.00)
5P GAIN MUTATION ANALYSIS 93 (16%) 490 0.824
(1.00) 		0.148
(1.00) 		0.257
(1.00) 		0.228
(1.00) 		0.728
(1.00) 		0.0306
(1.00) 		0.559
(1.00) 		0.91
(1.00) 		0.149
(1.00) 		0.641
(1.00) 		0.119
(1.00) 		0.18
(1.00)
5Q GAIN MUTATION ANALYSIS 59 (10%) 524 0.893
(1.00) 		0.958
(1.00) 		0.165
(1.00) 		0.724
(1.00) 		0.532
(1.00) 		0.355
(1.00) 		0.911
(1.00) 		0.583
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.817
(1.00)
6P GAIN MUTATION ANALYSIS 117 (20%) 466 0.374
(1.00) 		0.722
(1.00) 		0.161
(1.00) 		0.243
(1.00) 		0.527
(1.00) 		0.000986
(0.906) 		0.432
(1.00) 		0.408
(1.00) 		0.117
(1.00) 		0.000283
(0.266) 		0.275
(1.00) 		0.0237
(1.00)
7Q GAIN MUTATION ANALYSIS 299 (51%) 284 0.384
(1.00) 		0.351
(1.00) 		0.352
(1.00) 		0.000863
(0.796) 		0.616
(1.00) 		0.00118
(1.00) 		0.0208
(1.00) 		0.74
(1.00) 		0.0017
(1.00) 		0.506
(1.00) 		0.403
(1.00) 		0.0507
(1.00)
8P GAIN MUTATION ANALYSIS 164 (28%) 419 0.322
(1.00) 		0.576
(1.00) 		0.352
(1.00) 		0.487
(1.00) 		0.807
(1.00) 		0.335
(1.00) 		0.697
(1.00) 		0.782
(1.00) 		0.551
(1.00) 		0.277
(1.00) 		0.136
(1.00) 		0.306
(1.00)
8Q GAIN MUTATION ANALYSIS 294 (50%) 289 0.45
(1.00) 		0.268
(1.00) 		0.404
(1.00) 		0.403
(1.00) 		0.295
(1.00) 		0.255
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.0274
(1.00) 		0.0377
(1.00) 		0.149
(1.00) 		0.569
(1.00)
9P GAIN MUTATION ANALYSIS 113 (19%) 470 0.15
(1.00) 		0.74
(1.00) 		0.0453
(1.00) 		0.0133
(1.00) 		0.699
(1.00) 		0.0889
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.0172
(1.00) 		1
(1.00) 		0.266
(1.00) 		0.13
(1.00)
9Q GAIN MUTATION ANALYSIS 95 (16%) 488 0.269
(1.00) 		0.807
(1.00) 		0.258
(1.00) 		0.0243
(1.00) 		0.569
(1.00) 		0.252
(1.00) 		0.974
(1.00) 		0.574
(1.00) 		0.0927
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.294
(1.00)
10P GAIN MUTATION ANALYSIS 43 (7%) 540 0.129
(1.00) 		0.594
(1.00) 		0.86
(1.00) 		0.716
(1.00) 		0.213
(1.00) 		0.0551
(1.00) 		0.483
(1.00) 		0.753
(1.00) 		0.881
(1.00) 		0.501
(1.00) 		0.571
(1.00) 		0.234
(1.00)
10Q GAIN MUTATION ANALYSIS 24 (4%) 559 0.685
(1.00) 		0.0379
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.513
(1.00) 		0.00892
(1.00) 		0.713
(1.00) 		0.835
(1.00) 		0.915
(1.00) 		0.317
(1.00) 		0.66
(1.00) 		0.0716
(1.00)
11P GAIN MUTATION ANALYSIS 76 (13%) 507 0.929
(1.00) 		0.0105
(1.00) 		0.0515
(1.00) 		0.501
(1.00) 		0.268
(1.00) 		0.443
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.000294
(0.276) 		0.1
(1.00) 		0.399
(1.00) 		0.35
(1.00)
11Q GAIN MUTATION ANALYSIS 72 (12%) 511 0.756
(1.00) 		0.000646
(0.599) 		0.259
(1.00) 		0.577
(1.00) 		0.724
(1.00) 		0.571
(1.00) 		0.0404
(1.00) 		0.9
(1.00) 		0.00134
(1.00) 		0.307
(1.00) 		0.466
(1.00) 		0.698
(1.00)
12P GAIN MUTATION ANALYSIS 122 (21%) 461 0.489
(1.00) 		0.0414
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.317
(1.00) 		0.133
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.767
(1.00) 		0.405
(1.00) 		0.786
(1.00) 		0.682
(1.00)
12Q GAIN MUTATION ANALYSIS 103 (18%) 480 0.847
(1.00) 		0.00747
(1.00) 		0.0881
(1.00) 		0.0484
(1.00) 		0.442
(1.00) 		0.00977
(1.00) 		0.0528
(1.00) 		0.828
(1.00) 		0.226
(1.00) 		0.373
(1.00) 		0.67
(1.00) 		0.00308
(1.00)
15Q GAIN MUTATION ANALYSIS 17 (3%) 566 0.819
(1.00) 		0.148
(1.00) 		0.789
(1.00) 		0.502
(1.00) 		0.0469
(1.00) 		0.495
(1.00) 		0.398
(1.00) 		0.0132
(1.00) 		0.127
(1.00) 		0.235
(1.00) 		0.188
(1.00) 		0.355
(1.00)
16P GAIN MUTATION ANALYSIS 138 (24%) 445 0.686
(1.00) 		0.189
(1.00) 		1
(1.00) 		0.0252
(1.00) 		0.995
(1.00) 		0.00204
(1.00) 		0.26
(1.00) 		0.559
(1.00) 		0.00358
(1.00) 		0.448
(1.00) 		0.742
(1.00) 		0.212
(1.00)
16Q GAIN MUTATION ANALYSIS 134 (23%) 449 0.991
(1.00) 		0.0976
(1.00) 		0.741
(1.00) 		0.00884
(1.00) 		0.994
(1.00) 		0.000896
(0.825) 		0.232
(1.00) 		0.49
(1.00) 		0.00505
(1.00) 		0.436
(1.00) 		0.728
(1.00) 		0.453
(1.00)
17P GAIN MUTATION ANALYSIS 30 (5%) 553 0.126
(1.00) 		0.683
(1.00) 		0.834
(1.00) 		0.766
(1.00) 		0.585
(1.00) 		0.789
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.595
(1.00)
17Q GAIN MUTATION ANALYSIS 101 (17%) 482 0.339
(1.00) 		0.236
(1.00) 		0.903
(1.00) 		0.185
(1.00) 		0.802
(1.00) 		0.319
(1.00) 		0.0123
(1.00) 		0.743
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.274
(1.00) 		0.314
(1.00)
18P GAIN MUTATION ANALYSIS 31 (5%) 552 0.984
(1.00) 		0.74
(1.00) 		0.838
(1.00) 		0.00082
(0.758) 		0.802
(1.00) 		0.0518
(1.00) 		0.000851
(0.786) 		0.461
(1.00) 		0.0238
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.0692
(1.00)
18Q GAIN MUTATION ANALYSIS 19 (3%) 564 0.398
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.172
(1.00) 		0.354
(1.00) 		0.0839
(1.00) 		0.692
(1.00) 		0.244
(1.00) 		0.0512
(1.00) 		0.259
(1.00) 		0.613
(1.00) 		0.179
(1.00)
19P GAIN MUTATION ANALYSIS 91 (16%) 492 0.353
(1.00) 		0.83
(1.00) 		0.61
(1.00) 		0.767
(1.00) 		0.959
(1.00) 		0.119
(1.00) 		0.191
(1.00) 		0.171
(1.00) 		0.0828
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.415
(1.00)
19Q GAIN MUTATION ANALYSIS 100 (17%) 483 0.224
(1.00) 		0.968
(1.00) 		0.713
(1.00) 		0.708
(1.00) 		0.721
(1.00) 		0.203
(1.00) 		0.112
(1.00) 		0.509
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.471
(1.00) 		0.552
(1.00)
21Q GAIN MUTATION ANALYSIS 31 (5%) 552 0.201
(1.00) 		0.0362
(1.00) 		0.528
(1.00) 		0.95
(1.00) 		0.238
(1.00) 		0.686
(1.00) 		0.851
(1.00) 		0.855
(1.00) 		0.676
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.559
(1.00)
22Q GAIN MUTATION ANALYSIS 22 (4%) 561 0.977
(1.00) 		0.341
(1.00) 		0.0843
(1.00) 		0.892
(1.00) 		0.297
(1.00) 		0.397
(1.00) 		0.359
(1.00) 		1
(1.00) 		0.109
(1.00) 		0.294
(1.00) 		0.315
(1.00) 		0.263
(1.00)
XQ GAIN MUTATION ANALYSIS 104 (18%) 479 0.715
(1.00) 		0.175
(1.00) 		0.543
(1.00) 		0.163
(1.00) 		0.656
(1.00) 		0.426
(1.00) 		0.176
(1.00) 		0.329
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.812
(1.00)
1P LOSS MUTATION ANALYSIS 125 (21%) 458 0.147
(1.00) 		0.887
(1.00) 		0.142
(1.00) 		0.0402
(1.00) 		0.763
(1.00) 		0.00221
(1.00) 		0.00483
(1.00) 		0.762
(1.00) 		0.0295
(1.00) 		0.412
(1.00) 		0.341
(1.00) 		0.00913
(1.00)
1Q LOSS MUTATION ANALYSIS 67 (11%) 516 0.215
(1.00) 		0.666
(1.00) 		0.309
(1.00) 		0.405
(1.00) 		0.739
(1.00) 		0.0193
(1.00) 		0.0404
(1.00) 		0.12
(1.00) 		0.308
(1.00) 		0.0734
(1.00) 		0.37
(1.00) 		0.213
(1.00)
2P LOSS MUTATION ANALYSIS 17 (3%) 566 0.808
(1.00) 		0.104
(1.00) 		0.00125
(1.00) 		0.763
(1.00) 		0.85
(1.00) 		0.892
(1.00) 		0.84
(1.00) 		0.807
(1.00) 		0.0137
(1.00) 		0.235
(1.00) 		1
(1.00) 		0.956
(1.00)
2Q LOSS MUTATION ANALYSIS 14 (2%) 569 0.361
(1.00) 		0.416
(1.00) 		0.0694
(1.00) 		0.516
(1.00) 		0.804
(1.00) 		1
(1.00) 		0.627
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.907
(1.00)
3P LOSS MUTATION ANALYSIS 61 (10%) 522 0.0668
(1.00) 		0.962
(1.00) 		0.542
(1.00) 		0.0339
(1.00) 		0.0225
(1.00) 		0.055
(1.00) 		0.0017
(1.00) 		0.417
(1.00) 		0.0886
(1.00) 		0.241
(1.00) 		0.102
(1.00) 		0.102
(1.00)
3Q LOSS MUTATION ANALYSIS 38 (7%) 545 0.491
(1.00) 		0.453
(1.00) 		0.849
(1.00) 		0.0833
(1.00) 		0.0877
(1.00) 		0.561
(1.00) 		0.185
(1.00) 		0.243
(1.00) 		0.00812
(1.00) 		0.111
(1.00) 		0.299
(1.00) 		0.417
(1.00)
4P LOSS MUTATION ANALYSIS 181 (31%) 402 0.256
(1.00) 		0.697
(1.00) 		0.19
(1.00) 		0.0137
(1.00) 		0.72
(1.00) 		0.00137
(1.00) 		0.00506
(1.00) 		0.53
(1.00) 		0.0187
(1.00) 		0.00051
(0.475) 		0.123
(1.00) 		0.00962
(1.00)
4Q LOSS MUTATION ANALYSIS 175 (30%) 408 0.572
(1.00) 		0.982
(1.00) 		0.00572
(1.00) 		0.0967
(1.00) 		0.587
(1.00) 		0.00693
(1.00) 		0.249
(1.00) 		0.588
(1.00) 		0.00513
(1.00) 		0.000393
(0.367) 		0.852
(1.00) 		0.0284
(1.00)
5P LOSS MUTATION ANALYSIS 75 (13%) 508 0.533
(1.00) 		0.226
(1.00) 		0.267
(1.00) 		0.108
(1.00) 		0.81
(1.00) 		0.00637
(1.00) 		0.415
(1.00) 		0.62
(1.00) 		0.323
(1.00) 		0.0193
(1.00) 		0.27
(1.00) 		0.0386
(1.00)
5Q LOSS MUTATION ANALYSIS 109 (19%) 474 0.183
(1.00) 		0.427
(1.00) 		0.0423
(1.00) 		0.0896
(1.00) 		0.544
(1.00) 		0.00336
(1.00) 		0.122
(1.00) 		0.916
(1.00) 		0.0467
(1.00) 		0.00195
(1.00) 		0.487
(1.00) 		0.0256
(1.00)
6P LOSS MUTATION ANALYSIS 46 (8%) 537 0.118
(1.00) 		0.288
(1.00) 		0.73
(1.00) 		0.804
(1.00) 		0.212
(1.00) 		0.352
(1.00) 		0.614
(1.00) 		0.539
(1.00) 		0.151
(1.00) 		0.525
(1.00) 		0.0734
(1.00) 		0.208
(1.00)
6Q LOSS MUTATION ANALYSIS 68 (12%) 515 0.124
(1.00) 		0.974
(1.00) 		0.384
(1.00) 		0.0807
(1.00) 		0.109
(1.00) 		0.178
(1.00) 		0.043
(1.00) 		0.301
(1.00) 		0.0442
(1.00) 		1
(1.00) 		0.194
(1.00) 		0.062
(1.00)
8P LOSS MUTATION ANALYSIS 203 (35%) 380 0.867
(1.00) 		0.81
(1.00) 		0.00124
(1.00) 		0.0641
(1.00) 		0.234
(1.00) 		0.000752
(0.697) 		0.0965
(1.00) 		0.297
(1.00) 		0.000942
(0.867) 		0.288
(1.00) 		0.245
(1.00) 		0.00124
(1.00)
8Q LOSS MUTATION ANALYSIS 36 (6%) 547 0.916
(1.00) 		0.968
(1.00) 		0.442
(1.00) 		0.214
(1.00) 		0.48
(1.00) 		0.144
(1.00) 		0.15
(1.00) 		0.0579
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.114
(1.00)
9P LOSS MUTATION ANALYSIS 70 (12%) 513 0.0371
(1.00) 		0.323
(1.00) 		0.567
(1.00) 		0.86
(1.00) 		0.112
(1.00) 		0.508
(1.00) 		0.258
(1.00) 		0.307
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.0372
(1.00) 		0.348
(1.00)
9Q LOSS MUTATION ANALYSIS 69 (12%) 514 0.0211
(1.00) 		0.0317
(1.00) 		0.663
(1.00) 		0.702
(1.00) 		0.119
(1.00) 		0.461
(1.00) 		0.21
(1.00) 		0.7
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.0372
(1.00) 		0.809
(1.00)
10P LOSS MUTATION ANALYSIS 93 (16%) 490 0.231
(1.00) 		0.0057
(1.00) 		0.0978
(1.00) 		0.262
(1.00) 		0.949
(1.00) 		0.0132
(1.00) 		0.238
(1.00) 		0.822
(1.00) 		0.0253
(1.00) 		0.000796
(0.736) 		1
(1.00) 		0.161
(1.00)
10Q LOSS MUTATION ANALYSIS 100 (17%) 483 0.198
(1.00) 		0.00864
(1.00) 		0.0353
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.547
(1.00) 		0.826
(1.00) 		0.0171
(1.00) 		0.0012
(1.00) 		0.971
(1.00) 		0.341
(1.00)
11P LOSS MUTATION ANALYSIS 72 (12%) 511 0.772
(1.00) 		0.372
(1.00) 		0.323
(1.00) 		0.466
(1.00) 		0.32
(1.00) 		0.0105
(1.00) 		0.0332
(1.00) 		0.801
(1.00) 		0.217
(1.00) 		0.0877
(1.00) 		0.702
(1.00) 		0.0174
(1.00)
11Q LOSS MUTATION ANALYSIS 85 (15%) 498 0.449
(1.00) 		0.397
(1.00) 		0.347
(1.00) 		0.66
(1.00) 		0.403
(1.00) 		0.0322
(1.00) 		0.407
(1.00) 		0.725
(1.00) 		0.117
(1.00) 		0.0297
(1.00) 		0.945
(1.00) 		0.116
(1.00)
12P LOSS MUTATION ANALYSIS 59 (10%) 524 0.349
(1.00) 		0.712
(1.00) 		0.0641
(1.00) 		0.74
(1.00) 		0.253
(1.00) 		0.0559
(1.00) 		0.303
(1.00) 		0.493
(1.00) 		0.00307
(1.00) 		0.229
(1.00) 		0.941
(1.00) 		0.66
(1.00)
12Q LOSS MUTATION ANALYSIS 61 (10%) 522 0.56
(1.00) 		0.968
(1.00) 		0.171
(1.00) 		0.633
(1.00) 		0.413
(1.00) 		0.103
(1.00) 		0.176
(1.00) 		0.685
(1.00) 		0.0607
(1.00) 		0.241
(1.00) 		1
(1.00) 		0.6
(1.00)
13Q LOSS MUTATION ANALYSIS 19 (3%) 564 0.332
(1.00) 		0.96
(1.00) 		0.189
(1.00) 		0.608
(1.00) 		0.662
(1.00) 		0.0121
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.0242
(1.00) 		1
(1.00) 		1
(1.00) 		0.0803
(1.00)
15Q LOSS MUTATION ANALYSIS 209 (36%) 374 0.445
(1.00) 		0.693
(1.00) 		0.0516
(1.00) 		0.0449
(1.00) 		0.263
(1.00) 		0.0143
(1.00) 		0.211
(1.00) 		0.545
(1.00) 		0.00459
(1.00) 		0.0124
(1.00) 		0.377
(1.00) 		0.0456
(1.00)
16P LOSS MUTATION ANALYSIS 31 (5%) 552 0.0713
(1.00) 		0.855
(1.00) 		0.838
(1.00) 		0.126
(1.00) 		0.482
(1.00) 		0.821
(1.00) 		0.942
(1.00) 		0.198
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.565
(1.00) 		0.706
(1.00)
16Q LOSS MUTATION ANALYSIS 36 (6%) 547 0.237
(1.00) 		0.761
(1.00) 		0.124
(1.00) 		0.488
(1.00) 		0.876
(1.00) 		0.321
(1.00) 		0.923
(1.00) 		0.731
(1.00) 		0.341
(1.00) 		0.439
(1.00) 		0.929
(1.00) 		0.17
(1.00)
17Q LOSS MUTATION ANALYSIS 83 (14%) 500 0.701
(1.00) 		0.645
(1.00) 		0.352
(1.00) 		0.0928
(1.00) 		0.271
(1.00) 		0.0265
(1.00) 		0.282
(1.00) 		0.342
(1.00) 		0.654
(1.00) 		0.623
(1.00) 		0.8
(1.00) 		0.0749
(1.00)
19P LOSS MUTATION ANALYSIS 63 (11%) 520 0.257
(1.00) 		0.595
(1.00) 		0.0231
(1.00) 		0.000377
(0.353) 		0.899
(1.00) 		0.00143
(1.00) 		0.00519
(1.00) 		0.689
(1.00) 		0.0732
(1.00) 		0.253
(1.00) 		0.487
(1.00) 		0.00382
(1.00)
19Q LOSS MUTATION ANALYSIS 52 (9%) 531 0.664
(1.00) 		0.665
(1.00) 		0.0692
(1.00) 		0.000426
(0.397) 		0.959
(1.00) 		0.00346
(1.00) 		0.021
(1.00) 		0.308
(1.00) 		0.189
(1.00) 		0.188
(1.00) 		0.794
(1.00) 		0.0104
(1.00)
20P LOSS MUTATION ANALYSIS 62 (11%) 521 0.804
(1.00) 		0.436
(1.00) 		0.363
(1.00) 		0.843
(1.00) 		0.817
(1.00) 		0.715
(1.00) 		0.808
(1.00) 		0.591
(1.00) 		0.335
(1.00) 		0.608
(1.00) 		0.609
(1.00) 		0.884
(1.00)
20Q LOSS MUTATION ANALYSIS 6 (1%) 577 0.0927
(1.00) 		0.0203
(1.00) 		0.195
(1.00) 		0.857
(1.00) 		0.511
(1.00) 		0.39
(1.00) 		0.863
(1.00) 		0.691
(1.00) 		0.415
(1.00) 		1
(1.00) 		1
(1.00) 		0.97
(1.00)
21Q LOSS MUTATION ANALYSIS 178 (31%) 405 0.676
(1.00) 		0.554
(1.00) 		0.00459
(1.00) 		0.346
(1.00) 		0.912
(1.00) 		0.00898
(1.00) 		0.714
(1.00) 		0.787
(1.00) 		0.00217
(1.00) 		0.466
(1.00) 		0.783
(1.00) 		0.00136
(1.00)
XQ LOSS MUTATION ANALYSIS 76 (13%) 507 0.615
(1.00) 		0.319
(1.00) 		0.165
(1.00) 		0.17
(1.00) 		0.905
(1.00) 		0.198
(1.00) 		0.0315
(1.00) 		1
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.229
(1.00) 		0.258
(1.00)
'6Q GAIN MUTATION STATUS' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000136 (Fisher's exact test), Q value = 0.13

Table S1.  Gene #12: '6Q GAIN MUTATION STATUS' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 574
6Q GAIN MUTATED 7 98
6Q GAIN WILD-TYPE 2 476

Figure S1.  Get High-res Image Gene #12: '6Q GAIN MUTATION STATUS' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'7P GAIN MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00022 (Chi-square test), Q value = 0.21

Table S2.  Gene #13: '7P GAIN MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 100 1 41 156 10 3 27 22 75 49 59 25 1
7P GAIN MUTATED 55 1 19 68 3 2 13 15 54 34 40 19 0
7P GAIN WILD-TYPE 45 0 22 88 7 1 14 7 21 15 19 6 1

Figure S2.  Get High-res Image Gene #13: '7P GAIN MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'7P GAIN MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.022

Table S3.  Gene #13: '7P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
7P GAIN MUTATED 160 99 71
7P GAIN WILD-TYPE 169 46 35

Figure S3.  Get High-res Image Gene #13: '7P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'13Q GAIN MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-08 (Fisher's exact test), Q value = 1.3e-05

Table S4.  Gene #25: '13Q GAIN MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
13Q GAIN MUTATED 225 15 101 3
13Q GAIN WILD-TYPE 139 40 42 10

Figure S4.  Get High-res Image Gene #25: '13Q GAIN MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'14Q GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 0.000231 (Chi-square test), Q value = 0.22

Table S5.  Gene #26: '14Q GAIN MUTATION STATUS' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 440 72 9 1 52
14Q GAIN MUTATED 28 4 4 0 7
14Q GAIN WILD-TYPE 412 68 5 1 45

Figure S5.  Get High-res Image Gene #26: '14Q GAIN MUTATION STATUS' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'20P GAIN MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3e-06 (Fisher's exact test), Q value = 0.0029

Table S6.  Gene #36: '20P GAIN MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
20P GAIN MUTATED 209 18 101 4
20P GAIN WILD-TYPE 155 37 42 9

Figure S6.  Get High-res Image Gene #36: '20P GAIN MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'20Q GAIN MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0039

Table S7.  Gene #37: '20Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
20Q GAIN MUTATED 297 141
20Q GAIN WILD-TYPE 123 18

Figure S7.  Get High-res Image Gene #37: '20Q GAIN MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20Q GAIN MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.23e-12 (Fisher's exact test), Q value = 2.1e-09

Table S8.  Gene #37: '20Q GAIN MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
20Q GAIN MUTATED 272 24 132 7
20Q GAIN WILD-TYPE 92 31 11 6

Figure S8.  Get High-res Image Gene #37: '20Q GAIN MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'7P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.91e-25 (t-test), Q value = 2.8e-22

Table S9.  Gene #53: '7P LOSS MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 549 2.2 (4.7)
7P LOSS MUTATED 4 0.0 (0.0)
7P LOSS WILD-TYPE 545 2.2 (4.7)

Figure S9.  Get High-res Image Gene #53: '7P LOSS MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'7Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.17e-06 (t-test), Q value = 0.0021

Table S10.  Gene #54: '7Q LOSS MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 549 2.2 (4.7)
7Q LOSS MUTATED 5 0.2 (0.4)
7Q LOSS WILD-TYPE 544 2.2 (4.8)

Figure S10.  Get High-res Image Gene #54: '7Q LOSS MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'14Q LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.0019

Table S11.  Gene #66: '14Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
14Q LOSS MUTATED 118 4 60 1
14Q LOSS WILD-TYPE 246 51 83 12

Figure S11.  Get High-res Image Gene #66: '14Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'17P LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.0029

Table S12.  Gene #70: '17P LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
17P LOSS MUTATED 202 13 92 6
17P LOSS WILD-TYPE 162 42 51 7

Figure S12.  Get High-res Image Gene #70: '17P LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'18P LOSS MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.0015

Table S13.  Gene #72: '18P LOSS MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
18P LOSS MUTATED 232 122
18P LOSS WILD-TYPE 188 37

Figure S13.  Get High-res Image Gene #72: '18P LOSS MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18P LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.81e-16 (Fisher's exact test), Q value = 9.4e-13

Table S14.  Gene #72: '18P LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
18P LOSS MUTATED 222 9 115 7
18P LOSS WILD-TYPE 142 46 28 6

Figure S14.  Get High-res Image Gene #72: '18P LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'18Q LOSS MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.47e-08 (Fisher's exact test), Q value = 1.4e-05

Table S15.  Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
18Q LOSS MUTATED 249 133
18Q LOSS WILD-TYPE 171 26

Figure S15.  Get High-res Image Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18Q LOSS MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.91e-05 (Chi-square test), Q value = 0.065

Table S16.  Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 100 1 41 156 10 3 27 22 75 49 59 25 1
18Q LOSS MUTATED 56 0 22 95 4 3 14 18 54 37 50 22 0
18Q LOSS WILD-TYPE 44 1 19 61 6 0 13 4 21 12 9 3 1

Figure S16.  Get High-res Image Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'18Q LOSS MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.14

Table S17.  Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
18Q LOSS MUTATED 193 109 80
18Q LOSS WILD-TYPE 136 36 26

Figure S17.  Get High-res Image Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'18Q LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.39e-16 (Fisher's exact test), Q value = 4.2e-13

Table S18.  Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
18Q LOSS MUTATED 236 12 122 10
18Q LOSS WILD-TYPE 128 43 21 3

Figure S18.  Get High-res Image Gene #73: '18Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'22Q LOSS MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.028

Table S19.  Gene #79: '22Q LOSS MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
22Q LOSS MUTATED 80 64 41
22Q LOSS WILD-TYPE 249 81 65

Figure S19.  Get High-res Image Gene #79: '22Q LOSS MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 583

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 12

  • 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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle