Rectum Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 75 arm-level results and 11 clinical features across 162 patients, one significant finding detected with Q value < 0.25.

  • 20q gain 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 75 arm-level results and 11 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 GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test
20q gain 132 (81%) 30 0.0358
(1.00) 		0.13
(1.00) 		0.686
(1.00) 		2.52e-05
(0.0205) 		0.395
(1.00) 		0.193
(1.00) 		0.264
(1.00) 		0.192
(1.00) 		0.308
(1.00) 		0.166
(1.00) 		0.858
(1.00)
1p gain 4 (2%) 158 0.0152
(1.00) 		0.859
(1.00) 		0.332
(1.00) 		0.296
(1.00) 		0.0399
(1.00) 		0.0312
(1.00) 		1
(1.00) 		0.431
(1.00) 		1
(1.00) 		1
(1.00) 		0.364
(1.00)
1q gain 27 (17%) 135 0.417
(1.00) 		0.383
(1.00) 		0.53
(1.00) 		0.233
(1.00) 		0.00248
(1.00) 		0.133
(1.00) 		0.829
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.53
(1.00) 		0.063
(1.00)
2p gain 20 (12%) 142 0.284
(1.00) 		0.451
(1.00) 		0.0073
(1.00) 		0.221
(1.00) 		0.536
(1.00) 		0.265
(1.00) 		0.298
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.0697
(1.00) 		0.281
(1.00)
2q gain 21 (13%) 141 0.153
(1.00) 		0.443
(1.00) 		0.0174
(1.00) 		0.218
(1.00) 		0.231
(1.00) 		0.0589
(1.00) 		0.708
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.0863
(1.00) 		0.73
(1.00)
3p gain 17 (10%) 145 0.814
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.363
(1.00) 		0.841
(1.00) 		0.251
(1.00) 		0.0925
(1.00) 		0.261
(1.00) 		0.121
(1.00) 		0.762
(1.00) 		0.456
(1.00)
3q gain 23 (14%) 139 0.506
(1.00) 		0.668
(1.00) 		0.27
(1.00) 		0.218
(1.00) 		0.606
(1.00) 		0.296
(1.00) 		0.107
(1.00) 		0.406
(1.00) 		0.203
(1.00) 		0.301
(1.00) 		0.64
(1.00)
4p gain 4 (2%) 158 0.574
(1.00) 		0.233
(1.00) 		0.626
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.814
(1.00) 		0.252
(1.00) 		0.133
(1.00) 		1
(1.00) 		1
(1.00) 		0.00856
(1.00)
4q gain 3 (2%) 159 0.354
(1.00) 		0.251
(1.00) 		1
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.548
(1.00) 		0.877
(1.00) 		1
(1.00) 		0.0682
(1.00)
5p gain 20 (12%) 142 0.854
(1.00) 		0.0481
(1.00) 		0.638
(1.00) 		0.221
(1.00) 		0.744
(1.00) 		0.723
(1.00) 		0.335
(1.00) 		0.497
(1.00) 		0.552
(1.00) 		0.149
(1.00) 		0.14
(1.00)
5q gain 12 (7%) 150 0.462
(1.00) 		0.0508
(1.00) 		1
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.214
(1.00) 		0.36
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.302
(1.00)
6p gain 27 (17%) 135 0.858
(1.00) 		0.947
(1.00) 		0.834
(1.00) 		0.127
(1.00) 		0.851
(1.00) 		0.491
(1.00) 		0.374
(1.00) 		0.481
(1.00) 		0.0587
(1.00) 		0.0901
(1.00) 		0.459
(1.00)
6q gain 27 (17%) 135 0.228
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.128
(1.00) 		0.52
(1.00) 		0.306
(1.00) 		0.135
(1.00) 		0.146
(1.00) 		0.262
(1.00) 		0.103
(1.00) 		0.923
(1.00)
7p gain 90 (56%) 72 0.338
(1.00) 		0.363
(1.00) 		0.874
(1.00) 		0.00225
(1.00) 		0.18
(1.00) 		0.106
(1.00) 		0.804
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.0734
(1.00)
7q gain 79 (49%) 83 0.425
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.00232
(1.00) 		0.492
(1.00) 		0.046
(1.00) 		0.443
(1.00) 		0.0214
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.288
(1.00)
8p gain 27 (17%) 135 0.361
(1.00) 		0.15
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.846
(1.00) 		0.624
(1.00) 		0.713
(1.00) 		0.29
(1.00) 		0.591
(1.00) 		0.0349
(1.00) 		0.209
(1.00)
8q gain 72 (44%) 90 0.0685
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.145
(1.00) 		0.747
(1.00) 		0.228
(1.00) 		0.0966
(1.00) 		0.447
(1.00) 		0.228
(1.00) 		0.0128
(1.00) 		0.303
(1.00)
9p gain 35 (22%) 127 0.827
(1.00) 		0.296
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.542
(1.00) 		0.56
(1.00) 		0.418
(1.00) 		0.342
(1.00) 		0.863
(1.00) 		0.462
(1.00)
9q gain 26 (16%) 136 0.358
(1.00) 		0.0862
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.455
(1.00) 		0.807
(1.00) 		0.9
(1.00) 		0.293
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.798
(1.00)
10p gain 8 (5%) 154 0.993
(1.00) 		0.988
(1.00) 		0.471
(1.00) 		1
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.513
(1.00)
10q gain 4 (2%) 158 0.332
(1.00) 		0.171
(1.00) 		0.0416
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.316
(1.00) 		0.655
(1.00) 		0.774
(1.00) 		1
(1.00) 		1
(1.00) 		0.429
(1.00)
11p gain 21 (13%) 141 0.459
(1.00) 		0.195
(1.00) 		0.249
(1.00) 		0.218
(1.00) 		0.211
(1.00) 		0.951
(1.00) 		0.306
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.98
(1.00)
11q gain 17 (10%) 145 0.937
(1.00) 		0.0317
(1.00) 		0.8
(1.00) 		0.363
(1.00) 		0.144
(1.00) 		0.589
(1.00) 		0.198
(1.00) 		0.0863
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.0425
(1.00)
12p gain 28 (17%) 134 0.999
(1.00) 		0.0797
(1.00) 		1
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.373
(1.00) 		0.565
(1.00) 		0.731
(1.00) 		0.277
(1.00) 		0.691
(1.00) 		0.329
(1.00)
12q gain 19 (12%) 143 0.507
(1.00) 		0.0205
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.417
(1.00) 		0.9
(1.00) 		0.93
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.977
(1.00)
13q gain 102 (63%) 60 0.0286
(1.00) 		0.489
(1.00) 		0.871
(1.00) 		0.000377
(0.307) 		0.238
(1.00) 		0.037
(1.00) 		0.213
(1.00) 		0.178
(1.00) 		0.671
(1.00) 		0.865
(1.00) 		0.746
(1.00)
14q gain 4 (2%) 158 0.345
(1.00) 		0.447
(1.00) 		0.0416
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.112
(1.00) 		0.252
(1.00) 		0.76
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.0524
(1.00)
16p gain 29 (18%) 133 0.229
(1.00) 		0.636
(1.00) 		0.539
(1.00) 		0.129
(1.00) 		0.743
(1.00) 		0.508
(1.00) 		0.441
(1.00) 		0.571
(1.00) 		0.292
(1.00) 		0.588
(1.00) 		0.216
(1.00)
16q gain 30 (19%) 132 0.871
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.0747
(1.00) 		0.865
(1.00) 		0.211
(1.00) 		0.158
(1.00) 		0.375
(1.00) 		0.308
(1.00) 		0.813
(1.00) 		0.59
(1.00)
17p gain 3 (2%) 159 0.257
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.0728
(1.00) 		0.171
(1.00) 		0.548
(1.00) 		0.573
(1.00) 		1
(1.00)
17q gain 18 (11%) 144 0.652
(1.00) 		0.469
(1.00) 		0.621
(1.00) 		0.365
(1.00) 		0.751
(1.00) 		0.127
(1.00) 		0.459
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.5
(1.00) 		0.463
(1.00)
18p gain 7 (4%) 155 0.964
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.245
(1.00) 		0.262
(1.00) 		0.194
(1.00) 		0.47
(1.00) 		0.236
(1.00) 		0.487
(1.00) 		0.233
(1.00)
18q gain 4 (2%) 158 0.747
(1.00) 		0.626
(1.00) 		1
(1.00) 		0.0399
(1.00) 		0.0671
(1.00) 		0.0325
(1.00) 		0.0939
(1.00) 		0.141
(1.00) 		0.354
(1.00)
19p gain 20 (12%) 142 0.859
(1.00) 		0.365
(1.00) 		0.473
(1.00) 		0.221
(1.00) 		0.176
(1.00) 		0.856
(1.00) 		0.287
(1.00) 		0.385
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.861
(1.00)
19q gain 23 (14%) 139 0.827
(1.00) 		0.645
(1.00) 		0.27
(1.00) 		0.218
(1.00) 		0.188
(1.00) 		0.956
(1.00) 		0.148
(1.00) 		0.307
(1.00) 		0.595
(1.00) 		0.0769
(1.00) 		0.0358
(1.00)
20p gain 95 (59%) 67 0.874
(1.00) 		0.962
(1.00) 		0.2
(1.00) 		0.00182
(1.00) 		0.99
(1.00) 		0.209
(1.00) 		0.714
(1.00) 		0.536
(1.00) 		0.692
(1.00) 		0.172
(1.00) 		0.882
(1.00)
21q gain 7 (4%) 155 0.829
(1.00) 		0.0302
(1.00) 		0.703
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.586
(1.00) 		1
(1.00) 		0.553
(1.00) 		0.315
(1.00)
22q gain 5 (3%) 157 0.0152
(1.00) 		0.781
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.737
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.678
(1.00)
Xq gain 7 (4%) 155 0.808
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.0691
(1.00) 		0.191
(1.00) 		0.289
(1.00) 		0.0613
(1.00) 		1
(1.00) 		0.206
(1.00) 		0.293
(1.00)
1p loss 21 (13%) 141 0.806
(1.00) 		0.388
(1.00) 		0.105
(1.00) 		0.221
(1.00) 		0.459
(1.00) 		0.461
(1.00) 		0.93
(1.00) 		0.572
(1.00) 		0.571
(1.00) 		0.791
(1.00) 		0.975
(1.00)
1q loss 7 (4%) 155 0.789
(1.00) 		0.629
(1.00) 		0.455
(1.00) 		1
(1.00) 		1
(1.00) 		0.0231
(1.00) 		1
(1.00) 		0.0851
(1.00) 		0.236
(1.00) 		0.61
(1.00) 		0.55
(1.00)
2p loss 5 (3%) 157 0.611
(1.00) 		0.0489
(1.00) 		0.661
(1.00) 		0.296
(1.00) 		1
(1.00) 		1
(1.00) 		0.737
(1.00) 		1
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.707
(1.00)
3p loss 8 (5%) 154 0.849
(1.00) 		0.91
(1.00) 		0.292
(1.00) 		0.106
(1.00) 		0.425
(1.00) 		0.629
(1.00) 		0.161
(1.00) 		0.47
(1.00) 		0.266
(1.00) 		0.0274
(1.00) 		0.413
(1.00)
3q loss 4 (2%) 158 0.877
(1.00) 		0.766
(1.00) 		0.626
(1.00) 		0.00175
(1.00) 		0.774
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.76
(1.00) 		0.141
(1.00) 		0.041
(1.00) 		0.917
(1.00)
4p loss 39 (24%) 123 0.276
(1.00) 		0.132
(1.00) 		0.581
(1.00) 		0.304
(1.00) 		0.381
(1.00) 		0.433
(1.00) 		0.766
(1.00) 		0.717
(1.00) 		0.151
(1.00) 		0.423
(1.00) 		0.162
(1.00)
4q loss 46 (28%) 116 0.109
(1.00) 		0.306
(1.00) 		0.301
(1.00) 		0.188
(1.00) 		0.259
(1.00) 		0.676
(1.00) 		0.787
(1.00) 		0.91
(1.00) 		0.353
(1.00) 		0.583
(1.00) 		0.253
(1.00)
5p loss 11 (7%) 151 0.153
(1.00) 		0.788
(1.00) 		0.114
(1.00) 		0.601
(1.00) 		0.935
(1.00) 		0.378
(1.00) 		0.672
(1.00) 		0.919
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.255
(1.00)
5q loss 23 (14%) 139 0.58
(1.00) 		0.6
(1.00) 		0.27
(1.00) 		0.695
(1.00) 		0.55
(1.00) 		0.76
(1.00) 		0.414
(1.00) 		0.467
(1.00) 		0.00392
(1.00) 		0.368
(1.00) 		0.501
(1.00)
6p loss 8 (5%) 154 0.102
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.176
(1.00) 		1
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.747
(1.00)
6q loss 14 (9%) 148 0.657
(1.00) 		0.434
(1.00) 		0.577
(1.00) 		0.0643
(1.00) 		0.604
(1.00) 		0.162
(1.00) 		0.738
(1.00) 		0.36
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.343
(1.00)
8p loss 56 (35%) 106 0.268
(1.00) 		0.555
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.928
(1.00) 		0.427
(1.00) 		0.801
(1.00) 		0.183
(1.00) 		0.53
(1.00) 		0.128
(1.00)
8q loss 3 (2%) 159 0.679
(1.00) 		1
(1.00) 		1
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.0431
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.225
(1.00)
9p loss 12 (7%) 150 0.0169
(1.00) 		0.122
(1.00) 		1
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.852
(1.00) 		0.253
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.0169
(1.00) 		0.493
(1.00)
9q loss 11 (7%) 151 0.00797
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.592
(1.00) 		0.131
(1.00) 		0.713
(1.00) 		0.672
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.0169
(1.00) 		0.191
(1.00)
10p loss 17 (10%) 145 0.221
(1.00) 		0.00571
(1.00) 		1
(1.00) 		0.0377
(1.00) 		0.312
(1.00) 		0.403
(1.00) 		0.78
(1.00) 		0.982
(1.00) 		0.492
(1.00) 		0.63
(1.00) 		0.46
(1.00)
10q loss 21 (13%) 141 0.534
(1.00) 		0.0482
(1.00) 		0.491
(1.00) 		0.0773
(1.00) 		0.864
(1.00) 		0.901
(1.00) 		0.634
(1.00) 		0.785
(1.00) 		0.571
(1.00) 		0.61
(1.00) 		0.586
(1.00)
11p loss 19 (12%) 143 0.464
(1.00) 		0.578
(1.00) 		0.626
(1.00) 		0.046
(1.00) 		0.707
(1.00) 		0.584
(1.00) 		0.698
(1.00) 		0.0468
(1.00) 		0.533
(1.00) 		0.271
(1.00) 		0.279
(1.00)
11q loss 23 (14%) 139 0.353
(1.00) 		0.656
(1.00) 		0.508
(1.00) 		0.0137
(1.00) 		0.5
(1.00) 		0.794
(1.00) 		0.396
(1.00) 		0.278
(1.00) 		0.0379
(1.00) 		0.292
(1.00) 		0.93
(1.00)
12p loss 12 (7%) 150 0.177
(1.00) 		0.642
(1.00) 		0.0397
(1.00) 		0.601
(1.00) 		0.529
(1.00) 		0.368
(1.00) 		0.496
(1.00) 		0.374
(1.00) 		1
(1.00) 		1
(1.00) 		0.426
(1.00)
12q loss 8 (5%) 154 0.0971
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		0.908
(1.00) 		0.231
(1.00) 		0.245
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.487
(1.00) 		0.974
(1.00)
13q loss 5 (3%) 157 0.98
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.47
(1.00) 		0.273
(1.00) 		0.102
(1.00) 		0.551
(1.00) 		1
(1.00) 		1
(1.00) 		0.442
(1.00)
14q loss 51 (31%) 111 0.635
(1.00) 		0.881
(1.00) 		0.735
(1.00) 		0.00981
(1.00) 		0.266
(1.00) 		0.245
(1.00) 		0.503
(1.00) 		0.488
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.397
(1.00)
15q loss 58 (36%) 104 0.0719
(1.00) 		0.415
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.742
(1.00) 		0.923
(1.00) 		0.166
(1.00) 		0.668
(1.00) 		1
(1.00) 		0.0595
(1.00)
16p loss 6 (4%) 156 0.238
(1.00) 		0.413
(1.00) 		0.357
(1.00) 		0.641
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.0351
(1.00) 		1
(1.00) 		1
(1.00) 		0.259
(1.00)
16q loss 10 (6%) 152 0.877
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.0935
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.322
(1.00) 		1
(1.00) 		0.336
(1.00)
17p loss 89 (55%) 73 0.44
(1.00) 		0.0299
(1.00) 		0.527
(1.00) 		0.572
(1.00) 		0.133
(1.00) 		0.757
(1.00) 		0.435
(1.00) 		0.285
(1.00) 		0.691
(1.00) 		0.482
(1.00) 		0.647
(1.00)
17q loss 15 (9%) 147 0.465
(1.00) 		0.864
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.825
(1.00) 		1
(1.00) 		1
(1.00) 		0.0967
(1.00) 		0.596
(1.00) 		0.0587
(1.00)
18p loss 114 (70%) 48 0.65
(1.00) 		0.0737
(1.00) 		0.863
(1.00) 		0.00925
(1.00) 		0.0102
(1.00) 		0.487
(1.00) 		0.321
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.75
(1.00) 		0.462
(1.00)
18q loss 126 (78%) 36 0.407
(1.00) 		0.0453
(1.00) 		0.448
(1.00) 		0.482
(1.00) 		0.00609
(1.00) 		0.5
(1.00) 		0.603
(1.00) 		0.262
(1.00) 		0.615
(1.00) 		0.847
(1.00) 		0.59
(1.00)
19p loss 7 (4%) 155 0.0864
(1.00) 		0.794
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.88
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.678
(1.00) 		1
(1.00) 		1
(1.00) 		0.47
(1.00)
19q loss 7 (4%) 155 0.0462
(1.00) 		0.403
(1.00) 		1
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.778
(1.00) 		0.799
(1.00) 		0.181
(1.00) 		1
(1.00) 		1
(1.00) 		0.141
(1.00)
20p loss 18 (11%) 144 1
(1.00) 		0.689
(1.00) 		0.803
(1.00) 		0.636
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.503
(1.00)
21q loss 43 (27%) 119 0.162
(1.00) 		0.807
(1.00) 		0.476
(1.00) 		0.517
(1.00) 		0.291
(1.00) 		0.0616
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.656
(1.00) 		0.935
(1.00) 		0.0748
(1.00)
22q loss 42 (26%) 120 0.0236
(1.00) 		0.284
(1.00) 		0.475
(1.00) 		0.745
(1.00) 		0.628
(1.00) 		0.0953
(1.00) 		0.598
(1.00) 		0.244
(1.00) 		0.181
(1.00) 		0.662
(1.00) 		0.937
(1.00)
Xq loss 6 (4%) 156 0.518
(1.00) 		0.0974
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.846
(1.00) 		0.236
(1.00) 		0.221
(1.00) 		0.152
(1.00) 		1
(1.00) 		0.158
(1.00) 		0.652
(1.00)
'20q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.021

Table S1.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 143 13
20Q GAIN MUTATED 124 4
20Q GAIN WILD-TYPE 19 9

Figure S1.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 75

  • Number of selected clinical features = 11

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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