Correlation between copy number variations of arm-level result and selected clinical features
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
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/C14J0D2P
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 7 clinical features across 505 patients, 77 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 2p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 2q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 11p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 12p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 13q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 14q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 17q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18p gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'RACE'.

  • 18q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19p gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 19q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 20p gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 20q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 22q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 1p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 1q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 4p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 4q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 7p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 7q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 8p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 8q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 9p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 9q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 10p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 10q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 11p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 11q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 12p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 12q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.

  • 13q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 14q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 15q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 16p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

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

  • 17p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 17q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 18p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19p loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.

  • 19q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.

  • 21q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 22q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • xq loss cnv correlated to 'AGE' and '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 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 77 significant findings detected.

Clinical
Features
Time
to
Death
AGE HISTOLOGICAL
TYPE
RADIATIONS
RADIATION
REGIMENINDICATION
COMPLETENESS
OF
RESECTION
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
18p gain 68 (13%) 437 0.0728
(1.00)
0.0014
(0.664)
1e-05
(0.00554)
0.192
(1.00)
0.017
(1.00)
0.00035
(0.171)
0.691
(1.00)
19p gain 50 (10%) 455 0.105
(1.00)
1.24e-06
(0.00069)
1e-05
(0.00554)
0.246
(1.00)
0.727
(1.00)
0.0699
(1.00)
1
(1.00)
19q gain 50 (10%) 455 0.03
(1.00)
1.84e-07
(0.000103)
1e-05
(0.00554)
1
(1.00)
0.733
(1.00)
0.0153
(1.00)
0.376
(1.00)
20p gain 104 (21%) 401 0.0338
(1.00)
0.000155
(0.0758)
1e-05
(0.00554)
0.00193
(0.913)
0.0912
(1.00)
0.0732
(1.00)
1
(1.00)
20q gain 121 (24%) 384 0.00418
(1.00)
1.14e-05
(0.00573)
1e-05
(0.00554)
0.00225
(1.00)
0.0186
(1.00)
0.0137
(1.00)
0.501
(1.00)
4p loss 90 (18%) 415 0.0244
(1.00)
0.000157
(0.0766)
1e-05
(0.00554)
0.091
(1.00)
0.392
(1.00)
0.326
(1.00)
0.276
(1.00)
4q loss 92 (18%) 413 0.0152
(1.00)
5.93e-05
(0.0292)
1e-05
(0.00554)
0.0706
(1.00)
0.489
(1.00)
0.177
(1.00)
1
(1.00)
7p loss 41 (8%) 464 0.0413
(1.00)
5.63e-05
(0.0277)
1e-05
(0.00554)
0.277
(1.00)
0.315
(1.00)
0.0445
(1.00)
1
(1.00)
8p loss 73 (14%) 432 0.125
(1.00)
4.51e-05
(0.0225)
1e-05
(0.00554)
0.887
(1.00)
0.365
(1.00)
0.0557
(1.00)
0.702
(1.00)
9p loss 93 (18%) 412 0.0263
(1.00)
1.79e-05
(0.009)
1e-05
(0.00554)
0.607
(1.00)
0.0342
(1.00)
0.65
(1.00)
1
(1.00)
9q loss 111 (22%) 394 0.0365
(1.00)
5.99e-09
(3.35e-06)
1e-05
(0.00554)
0.336
(1.00)
0.191
(1.00)
0.249
(1.00)
0.741
(1.00)
12q loss 32 (6%) 473 0.000482
(0.234)
0.0685
(1.00)
1e-05
(0.00554)
0.31
(1.00)
0.628
(1.00)
0.405
(1.00)
0.563
(1.00)
15q loss 100 (20%) 405 0.00907
(1.00)
5.19e-06
(0.00288)
1e-05
(0.00554)
0.0445
(1.00)
0.332
(1.00)
0.175
(1.00)
1
(1.00)
16p loss 89 (18%) 416 0.0299
(1.00)
3.21e-05
(0.0161)
1e-05
(0.00554)
0.19
(1.00)
0.0121
(1.00)
0.104
(1.00)
0.472
(1.00)
16q loss 127 (25%) 378 0.0666
(1.00)
8.83e-07
(0.000493)
1e-05
(0.00554)
0.0846
(1.00)
0.0262
(1.00)
0.0344
(1.00)
1
(1.00)
17p loss 116 (23%) 389 0.00551
(1.00)
4.85e-06
(0.0027)
1e-05
(0.00554)
0.408
(1.00)
0.133
(1.00)
0.0112
(1.00)
0.508
(1.00)
17q loss 84 (17%) 421 0.0778
(1.00)
0.000125
(0.0613)
1e-05
(0.00554)
0.348
(1.00)
0.347
(1.00)
0.305
(1.00)
0.0495
(1.00)
19p loss 54 (11%) 451 0.000485
(0.235)
0.108
(1.00)
1e-05
(0.00554)
0.873
(1.00)
0.0709
(1.00)
0.619
(1.00)
0.154
(1.00)
19q loss 52 (10%) 453 0.000444
(0.216)
0.158
(1.00)
1e-05
(0.00554)
0.328
(1.00)
0.154
(1.00)
0.386
(1.00)
0.128
(1.00)
22q loss 100 (20%) 405 0.0604
(1.00)
4.87e-05
(0.0243)
1e-05
(0.00554)
0.0445
(1.00)
0.528
(1.00)
0.138
(1.00)
0.16
(1.00)
xq loss 65 (13%) 440 0.0132
(1.00)
0.000367
(0.179)
1e-05
(0.00554)
0.101
(1.00)
0.151
(1.00)
0.16
(1.00)
0.0832
(1.00)
1p gain 43 (9%) 462 0.00346
(1.00)
0.125
(1.00)
1e-05
(0.00554)
0.0479
(1.00)
0.048
(1.00)
0.0885
(1.00)
1
(1.00)
2p gain 87 (17%) 418 0.00238
(1.00)
0.00728
(1.00)
1e-05
(0.00554)
0.356
(1.00)
0.604
(1.00)
0.766
(1.00)
0.136
(1.00)
2q gain 71 (14%) 434 0.00613
(1.00)
0.0601
(1.00)
1e-05
(0.00554)
0.251
(1.00)
0.296
(1.00)
0.821
(1.00)
0.229
(1.00)
3q gain 74 (15%) 431 0.00258
(1.00)
0.0122
(1.00)
1e-05
(0.00554)
0.4
(1.00)
0.228
(1.00)
0.0102
(1.00)
1
(1.00)
5p gain 48 (10%) 457 0.000527
(0.255)
0.0158
(1.00)
1e-05
(0.00554)
0.0407
(1.00)
0.104
(1.00)
0.12
(1.00)
0.376
(1.00)
6p gain 73 (14%) 432 0.79
(1.00)
0.0523
(1.00)
1e-05
(0.00554)
0.478
(1.00)
0.334
(1.00)
0.0392
(1.00)
1
(1.00)
6q gain 59 (12%) 446 0.91
(1.00)
0.101
(1.00)
3e-05
(0.0151)
0.758
(1.00)
0.193
(1.00)
0.00509
(1.00)
1
(1.00)
11p gain 21 (4%) 484 0.0894
(1.00)
0.142
(1.00)
5e-05
(0.0248)
0.808
(1.00)
0.201
(1.00)
0.336
(1.00)
0.428
(1.00)
12p gain 65 (13%) 440 0.106
(1.00)
0.5
(1.00)
5e-05
(0.0248)
0.181
(1.00)
0.672
(1.00)
0.0372
(1.00)
0.229
(1.00)
13q gain 29 (6%) 476 0.801
(1.00)
0.00836
(1.00)
1e-05
(0.00554)
1
(1.00)
0.221
(1.00)
0.311
(1.00)
1
(1.00)
14q gain 36 (7%) 469 0.266
(1.00)
0.273
(1.00)
1e-05
(0.00554)
0.0061
(1.00)
0.216
(1.00)
0.356
(1.00)
1
(1.00)
17q gain 28 (6%) 477 0.019
(1.00)
0.282
(1.00)
5e-05
(0.0248)
1
(1.00)
0.0319
(1.00)
0.00623
(1.00)
0.563
(1.00)
18q gain 41 (8%) 464 0.00489
(1.00)
0.0342
(1.00)
1e-05
(0.00554)
0.47
(1.00)
0.00772
(1.00)
0.237
(1.00)
1
(1.00)
21q gain 35 (7%) 470 0.131
(1.00)
0.00344
(1.00)
1e-05
(0.00554)
0.237
(1.00)
0.376
(1.00)
0.195
(1.00)
1
(1.00)
22q gain 29 (6%) 476 0.0497
(1.00)
0.00292
(1.00)
1e-05
(0.00554)
0.831
(1.00)
0.02
(1.00)
0.115
(1.00)
1
(1.00)
1p loss 24 (5%) 481 0.742
(1.00)
0.0631
(1.00)
1e-05
(0.00554)
1
(1.00)
0.00357
(1.00)
0.721
(1.00)
1
(1.00)
1q loss 14 (3%) 491 0.0768
(1.00)
0.272
(1.00)
3e-05
(0.0151)
0.369
(1.00)
0.0227
(1.00)
0.398
(1.00)
1
(1.00)
3p loss 46 (9%) 459 0.146
(1.00)
0.00709
(1.00)
1e-05
(0.00554)
0.729
(1.00)
0.909
(1.00)
0.6
(1.00)
0.62
(1.00)
3q loss 29 (6%) 476 0.689
(1.00)
0.0436
(1.00)
1e-05
(0.00554)
0.284
(1.00)
0.444
(1.00)
0.115
(1.00)
1
(1.00)
5p loss 50 (10%) 455 0.0153
(1.00)
0.158
(1.00)
1e-05
(0.00554)
0.18
(1.00)
0.0989
(1.00)
0.306
(1.00)
0.12
(1.00)
5q loss 69 (14%) 436 0.0137
(1.00)
0.00132
(0.626)
1e-05
(0.00554)
0.562
(1.00)
0.539
(1.00)
0.273
(1.00)
0.0832
(1.00)
6p loss 16 (3%) 489 0.679
(1.00)
0.103
(1.00)
1e-05
(0.00554)
0.777
(1.00)
0.544
(1.00)
0.706
(1.00)
0.334
(1.00)
6q loss 24 (5%) 481 0.583
(1.00)
0.171
(1.00)
1e-05
(0.00554)
0.817
(1.00)
0.456
(1.00)
0.827
(1.00)
0.47
(1.00)
7q loss 40 (8%) 465 0.495
(1.00)
0.00119
(0.567)
1e-05
(0.00554)
0.356
(1.00)
0.524
(1.00)
0.241
(1.00)
1
(1.00)
8q loss 23 (5%) 482 0.651
(1.00)
0.199
(1.00)
1e-05
(0.00554)
0.638
(1.00)
0.528
(1.00)
0.221
(1.00)
0.47
(1.00)
10p loss 37 (7%) 468 0.195
(1.00)
0.00968
(1.00)
1e-05
(0.00554)
0.337
(1.00)
0.121
(1.00)
0.0369
(1.00)
0.61
(1.00)
10q loss 35 (7%) 470 0.401
(1.00)
0.00621
(1.00)
1e-05
(0.00554)
0.237
(1.00)
0.489
(1.00)
0.209
(1.00)
0.611
(1.00)
11p loss 68 (13%) 437 0.0136
(1.00)
0.00109
(0.52)
1e-05
(0.00554)
0.028
(1.00)
0.295
(1.00)
0.121
(1.00)
0.691
(1.00)
11q loss 66 (13%) 439 0.0281
(1.00)
0.004
(1.00)
1e-05
(0.00554)
0.00275
(1.00)
0.108
(1.00)
0.0676
(1.00)
0.397
(1.00)
12p loss 40 (8%) 465 0.00105
(0.501)
0.0644
(1.00)
1e-05
(0.00554)
0.195
(1.00)
0.0533
(1.00)
0.393
(1.00)
1
(1.00)
13q loss 83 (16%) 422 0.0339
(1.00)
0.0214
(1.00)
1e-05
(0.00554)
0.0431
(1.00)
0.461
(1.00)
0.62
(1.00)
0.266
(1.00)
14q loss 57 (11%) 448 0.0252
(1.00)
0.00384
(1.00)
1e-05
(0.00554)
0.434
(1.00)
0.693
(1.00)
0.0102
(1.00)
0.136
(1.00)
18p loss 46 (9%) 459 0.346
(1.00)
0.0287
(1.00)
5e-05
(0.0248)
0.297
(1.00)
0.165
(1.00)
0.988
(1.00)
1
(1.00)
18q loss 58 (11%) 447 0.453
(1.00)
0.0211
(1.00)
1e-05
(0.00554)
0.274
(1.00)
0.184
(1.00)
0.267
(1.00)
0.679
(1.00)
21q loss 51 (10%) 454 0.0241
(1.00)
0.00785
(1.00)
1e-05
(0.00554)
1
(1.00)
0.28
(1.00)
0.339
(1.00)
1
(1.00)
1q gain 173 (34%) 332 0.128
(1.00)
0.026
(1.00)
0.637
(1.00)
0.834
(1.00)
0.988
(1.00)
0.692
(1.00)
0.15
(1.00)
3p gain 44 (9%) 461 0.0686
(1.00)
0.406
(1.00)
0.00089
(0.428)
0.0337
(1.00)
0.347
(1.00)
0.0157
(1.00)
1
(1.00)
4p gain 14 (3%) 491 0.115
(1.00)
0.00994
(1.00)
0.00148
(0.702)
1
(1.00)
0.135
(1.00)
0.0189
(1.00)
0.282
(1.00)
4q gain 8 (2%) 497 0.641
(1.00)
0.428
(1.00)
0.0183
(1.00)
0.69
(1.00)
0.486
(1.00)
0.285
(1.00)
0.136
(1.00)
5q gain 18 (4%) 487 0.15
(1.00)
0.696
(1.00)
0.00278
(1.00)
0.422
(1.00)
0.229
(1.00)
0.474
(1.00)
1
(1.00)
7p gain 61 (12%) 444 0.0337
(1.00)
0.187
(1.00)
0.0678
(1.00)
0.287
(1.00)
0.692
(1.00)
0.868
(1.00)
1
(1.00)
7q gain 57 (11%) 448 0.00104
(0.499)
0.246
(1.00)
0.304
(1.00)
0.159
(1.00)
0.518
(1.00)
0.743
(1.00)
1
(1.00)
8p gain 112 (22%) 393 0.0578
(1.00)
0.0855
(1.00)
0.749
(1.00)
0.0721
(1.00)
0.166
(1.00)
0.575
(1.00)
0.741
(1.00)
8q gain 146 (29%) 359 0.0112
(1.00)
0.891
(1.00)
0.00356
(1.00)
0.0608
(1.00)
0.253
(1.00)
0.81
(1.00)
0.359
(1.00)
9p gain 20 (4%) 485 0.718
(1.00)
0.979
(1.00)
0.0736
(1.00)
0.306
(1.00)
0.365
(1.00)
0.44
(1.00)
0.0104
(1.00)
9q gain 7 (1%) 498 0.684
(1.00)
0.928
(1.00)
0.201
(1.00)
0.68
(1.00)
0.192
(1.00)
0.0726
(1.00)
0.168
(1.00)
10p gain 110 (22%) 395 0.843
(1.00)
0.19
(1.00)
0.726
(1.00)
0.545
(1.00)
0.805
(1.00)
0.187
(1.00)
0.312
(1.00)
10q gain 104 (21%) 401 0.579
(1.00)
0.693
(1.00)
0.787
(1.00)
0.622
(1.00)
0.33
(1.00)
0.196
(1.00)
1
(1.00)
11q gain 18 (4%) 487 0.00317
(1.00)
0.266
(1.00)
0.0132
(1.00)
0.79
(1.00)
0.276
(1.00)
0.557
(1.00)
1
(1.00)
12q gain 51 (10%) 454 0.106
(1.00)
0.54
(1.00)
0.0701
(1.00)
0.135
(1.00)
0.567
(1.00)
0.044
(1.00)
0.376
(1.00)
15q gain 10 (2%) 495 0.00935
(1.00)
0.421
(1.00)
0.645
(1.00)
0.299
(1.00)
0.103
(1.00)
0.386
(1.00)
0.282
(1.00)
16p gain 26 (5%) 479 0.536
(1.00)
0.0209
(1.00)
0.0187
(1.00)
0.0717
(1.00)
0.275
(1.00)
0.0823
(1.00)
0.509
(1.00)
16q gain 9 (2%) 496 0.948
(1.00)
0.138
(1.00)
0.168
(1.00)
0.455
(1.00)
0.00082
(0.395)
0.186
(1.00)
0.227
(1.00)
17p gain 11 (2%) 494 0.906
(1.00)
0.665
(1.00)
0.152
(1.00)
1
(1.00)
0.204
(1.00)
0.847
(1.00)
0.282
(1.00)
xq gain 60 (12%) 445 0.00912
(1.00)
0.287
(1.00)
0.296
(1.00)
0.538
(1.00)
0.232
(1.00)
1
(1.00)
1
(1.00)
2p loss 11 (2%) 494 0.0326
(1.00)
0.174
(1.00)
0.447
(1.00)
0.0405
(1.00)
0.106
(1.00)
0.386
(1.00)
0.309
(1.00)
2q loss 17 (3%) 488 0.00414
(1.00)
0.0891
(1.00)
0.337
(1.00)
0.0509
(1.00)
0.383
(1.00)
0.482
(1.00)
0.428
(1.00)
20p loss 16 (3%) 489 0.585
(1.00)
0.115
(1.00)
0.00995
(1.00)
0.0478
(1.00)
0.137
(1.00)
0.398
(1.00)
0.359
(1.00)
20q loss 8 (2%) 497 0.277
(1.00)
0.588
(1.00)
0.00946
(1.00)
0.0384
(1.00)
1
(1.00)
0.477
(1.00)
1
(1.00)
'1p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S1.  Gene #1: '1p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
1P GAIN MUTATED 18 2 23
1P GAIN WILD-TYPE 362 19 81

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'2p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S2.  Gene #3: '2p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
2P GAIN MUTATED 41 5 41
2P GAIN WILD-TYPE 339 16 63

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'2q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S3.  Gene #4: '2q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
2Q GAIN MUTATED 35 4 32
2Q GAIN WILD-TYPE 345 17 72

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S4.  Gene #6: '3q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
3Q GAIN MUTATED 32 4 38
3Q GAIN WILD-TYPE 348 17 66

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S5.  Gene #9: '5p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
5P GAIN MUTATED 16 3 29
5P GAIN WILD-TYPE 364 18 75

Figure S5.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S6.  Gene #11: '6p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
6P GAIN MUTATED 35 1 37
6P GAIN WILD-TYPE 345 20 67

Figure S6.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6q gain' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S7.  Gene #12: '6q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
6Q GAIN MUTATED 31 1 27
6Q GAIN WILD-TYPE 349 20 77

Figure S7.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p gain' versus 'HISTOLOGICAL.TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S8.  Gene #21: '11p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
11P GAIN MUTATED 7 0 14
11P GAIN WILD-TYPE 373 21 90

Figure S8.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p gain' versus 'HISTOLOGICAL.TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S9.  Gene #23: '12p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
12P GAIN MUTATED 34 3 28
12P GAIN WILD-TYPE 346 18 76

Figure S9.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S10.  Gene #25: '13q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
13Q GAIN MUTATED 8 1 20
13Q GAIN WILD-TYPE 372 20 84

Figure S10.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S11.  Gene #26: '14q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
14Q GAIN MUTATED 14 2 20
14Q GAIN WILD-TYPE 366 19 84

Figure S11.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q gain' versus 'HISTOLOGICAL.TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S12.  Gene #31: '17q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
17Q GAIN MUTATED 12 0 16
17Q GAIN WILD-TYPE 368 21 88

Figure S12.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S13.  Gene #32: '18p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
18P GAIN MUTATED 20 5 43
18P GAIN WILD-TYPE 360 16 61

Figure S13.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18p gain' versus 'RACE'

P value = 0.00035 (Fisher's exact test), Q value = 0.17

Table S14.  Gene #32: '18p gain' versus Clinical Feature #6: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 4 19 90 9 357
18P GAIN MUTATED 0 2 26 1 35
18P GAIN WILD-TYPE 4 17 64 8 322

Figure S14.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'RACE'

'18q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S15.  Gene #33: '18q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
18Q GAIN MUTATED 15 4 22
18Q GAIN WILD-TYPE 365 17 82

Figure S15.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p gain' versus 'AGE'

P value = 1.24e-06 (Wilcoxon-test), Q value = 0.00069

Table S16.  Gene #34: '19p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
19P GAIN MUTATED 50 70.6 (8.7)
19P GAIN WILD-TYPE 454 63.1 (11.2)

Figure S16.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'AGE'

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S17.  Gene #34: '19p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
19P GAIN MUTATED 19 3 28
19P GAIN WILD-TYPE 361 18 76

Figure S17.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q gain' versus 'AGE'

P value = 1.84e-07 (Wilcoxon-test), Q value = 1e-04

Table S18.  Gene #35: '19q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
19Q GAIN MUTATED 50 71.1 (8.7)
19Q GAIN WILD-TYPE 454 63.0 (11.2)

Figure S18.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'AGE'

'19q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S19.  Gene #35: '19q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
19Q GAIN MUTATED 13 3 34
19Q GAIN WILD-TYPE 367 18 70

Figure S19.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'AGE'

P value = 0.000155 (Wilcoxon-test), Q value = 0.076

Table S20.  Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
20P GAIN MUTATED 104 67.3 (10.0)
20P GAIN WILD-TYPE 400 62.9 (11.3)

Figure S20.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S21.  Gene #36: '20p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
20P GAIN MUTATED 45 4 55
20P GAIN WILD-TYPE 335 17 49

Figure S21.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'AGE'

P value = 1.14e-05 (Wilcoxon-test), Q value = 0.0057

Table S22.  Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
20Q GAIN MUTATED 121 67.5 (10.0)
20Q GAIN WILD-TYPE 383 62.7 (11.3)

Figure S22.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S23.  Gene #37: '20q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
20Q GAIN MUTATED 52 4 65
20Q GAIN WILD-TYPE 328 17 39

Figure S23.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S24.  Gene #38: '21q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
21Q GAIN MUTATED 11 1 23
21Q GAIN WILD-TYPE 369 20 81

Figure S24.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S25.  Gene #39: '22q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
22Q GAIN MUTATED 7 1 21
22Q GAIN WILD-TYPE 373 20 83

Figure S25.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'1p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S26.  Gene #41: '1p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
1P LOSS MUTATED 6 3 15
1P LOSS WILD-TYPE 374 18 89

Figure S26.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'1q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S27.  Gene #42: '1q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
1Q LOSS MUTATED 3 2 9
1Q LOSS WILD-TYPE 377 19 95

Figure S27.  Get High-res Image Gene #42: '1q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S28.  Gene #45: '3p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
3P LOSS MUTATED 16 6 24
3P LOSS WILD-TYPE 364 15 80

Figure S28.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S29.  Gene #46: '3q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
3Q LOSS MUTATED 10 2 17
3Q LOSS WILD-TYPE 370 19 87

Figure S29.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4p loss' versus 'AGE'

P value = 0.000157 (Wilcoxon-test), Q value = 0.077

Table S30.  Gene #47: '4p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
4P LOSS MUTATED 90 67.8 (9.6)
4P LOSS WILD-TYPE 414 63.0 (11.4)

Figure S30.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'AGE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S31.  Gene #47: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
4P LOSS MUTATED 29 6 55
4P LOSS WILD-TYPE 351 15 49

Figure S31.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'AGE'

P value = 5.93e-05 (Wilcoxon-test), Q value = 0.029

Table S32.  Gene #48: '4q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
4Q LOSS MUTATED 92 67.9 (9.7)
4Q LOSS WILD-TYPE 412 62.9 (11.3)

Figure S32.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #2: 'AGE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S33.  Gene #48: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
4Q LOSS MUTATED 30 7 55
4Q LOSS WILD-TYPE 350 14 49

Figure S33.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S34.  Gene #49: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
5P LOSS MUTATED 16 1 33
5P LOSS WILD-TYPE 364 20 71

Figure S34.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S35.  Gene #50: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
5Q LOSS MUTATED 19 4 46
5Q LOSS WILD-TYPE 361 17 58

Figure S35.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S36.  Gene #51: '6p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
6P LOSS MUTATED 3 1 12
6P LOSS WILD-TYPE 377 20 92

Figure S36.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S37.  Gene #52: '6q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
6Q LOSS MUTATED 4 1 19
6Q LOSS WILD-TYPE 376 20 85

Figure S37.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7p loss' versus 'AGE'

P value = 5.63e-05 (Wilcoxon-test), Q value = 0.028

Table S38.  Gene #53: '7p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
7P LOSS MUTATED 41 69.9 (9.7)
7P LOSS WILD-TYPE 463 63.3 (11.2)

Figure S38.  Get High-res Image Gene #53: '7p loss' versus Clinical Feature #2: 'AGE'

'7p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S39.  Gene #53: '7p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
7P LOSS MUTATED 14 2 25
7P LOSS WILD-TYPE 366 19 79

Figure S39.  Get High-res Image Gene #53: '7p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S40.  Gene #54: '7q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
7Q LOSS MUTATED 8 2 30
7Q LOSS WILD-TYPE 372 19 74

Figure S40.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss' versus 'AGE'

P value = 4.51e-05 (Wilcoxon-test), Q value = 0.023

Table S41.  Gene #55: '8p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
8P LOSS MUTATED 73 68.2 (8.6)
8P LOSS WILD-TYPE 431 63.1 (11.4)

Figure S41.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #2: 'AGE'

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S42.  Gene #55: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
8P LOSS MUTATED 15 4 54
8P LOSS WILD-TYPE 365 17 50

Figure S42.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S43.  Gene #56: '8q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
8Q LOSS MUTATED 2 1 20
8Q LOSS WILD-TYPE 378 20 84

Figure S43.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'AGE'

P value = 1.79e-05 (Wilcoxon-test), Q value = 0.009

Table S44.  Gene #57: '9p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
9P LOSS MUTATED 93 67.9 (8.6)
9P LOSS WILD-TYPE 411 62.9 (11.5)

Figure S44.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'AGE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S45.  Gene #57: '9p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
9P LOSS MUTATED 34 8 51
9P LOSS WILD-TYPE 346 13 53

Figure S45.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss' versus 'AGE'

P value = 5.99e-09 (Wilcoxon-test), Q value = 3.4e-06

Table S46.  Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
9Q LOSS MUTATED 111 69.0 (8.8)
9Q LOSS WILD-TYPE 393 62.4 (11.4)

Figure S46.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

'9q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S47.  Gene #58: '9q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
9Q LOSS MUTATED 46 9 56
9Q LOSS WILD-TYPE 334 12 48

Figure S47.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S48.  Gene #59: '10p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
10P LOSS MUTATED 9 4 24
10P LOSS WILD-TYPE 371 17 80

Figure S48.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S49.  Gene #60: '10q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
10Q LOSS MUTATED 12 4 19
10Q LOSS WILD-TYPE 368 17 85

Figure S49.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S50.  Gene #61: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
11P LOSS MUTATED 25 6 37
11P LOSS WILD-TYPE 355 15 67

Figure S50.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S51.  Gene #62: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
11Q LOSS MUTATED 22 7 37
11Q LOSS WILD-TYPE 358 14 67

Figure S51.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S52.  Gene #63: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
12P LOSS MUTATED 13 1 26
12P LOSS WILD-TYPE 367 20 78

Figure S52.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12q loss' versus 'Time to Death'

P value = 0.000482 (logrank test), Q value = 0.23

Table S53.  Gene #64: '12q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 503 60 0.0 - 191.8 (22.8)
12Q LOSS MUTATED 32 9 0.8 - 97.7 (18.5)
12Q LOSS WILD-TYPE 471 51 0.0 - 191.8 (23.3)

Figure S53.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #1: 'Time to Death'

'12q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S54.  Gene #64: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
12Q LOSS MUTATED 8 1 23
12Q LOSS WILD-TYPE 372 20 81

Figure S54.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S55.  Gene #65: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
13Q LOSS MUTATED 44 5 34
13Q LOSS WILD-TYPE 336 16 70

Figure S55.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S56.  Gene #66: '14q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
14Q LOSS MUTATED 19 3 35
14Q LOSS WILD-TYPE 361 18 69

Figure S56.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss' versus 'AGE'

P value = 5.19e-06 (Wilcoxon-test), Q value = 0.0029

Table S57.  Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
15Q LOSS MUTATED 100 68.3 (10.3)
15Q LOSS WILD-TYPE 404 62.7 (11.2)

Figure S57.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

'15q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S58.  Gene #67: '15q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
15Q LOSS MUTATED 35 8 57
15Q LOSS WILD-TYPE 345 13 47

Figure S58.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss' versus 'AGE'

P value = 3.21e-05 (Wilcoxon-test), Q value = 0.016

Table S59.  Gene #68: '16p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
16P LOSS MUTATED 89 67.9 (9.7)
16P LOSS WILD-TYPE 415 63.0 (11.3)

Figure S59.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #2: 'AGE'

'16p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S60.  Gene #68: '16p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
16P LOSS MUTATED 31 6 52
16P LOSS WILD-TYPE 349 15 52

Figure S60.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'AGE'

P value = 8.83e-07 (Wilcoxon-test), Q value = 0.00049

Table S61.  Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
16Q LOSS MUTATED 127 67.8 (9.4)
16Q LOSS WILD-TYPE 377 62.5 (11.5)

Figure S61.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S62.  Gene #69: '16q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
16Q LOSS MUTATED 51 7 69
16Q LOSS WILD-TYPE 329 14 35

Figure S62.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'AGE'

P value = 4.85e-06 (Wilcoxon-test), Q value = 0.0027

Table S63.  Gene #70: '17p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
17P LOSS MUTATED 116 67.7 (9.1)
17P LOSS WILD-TYPE 388 62.7 (11.5)

Figure S63.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #2: 'AGE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S64.  Gene #70: '17p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
17P LOSS MUTATED 41 9 66
17P LOSS WILD-TYPE 339 12 38

Figure S64.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss' versus 'AGE'

P value = 0.000125 (Wilcoxon-test), Q value = 0.061

Table S65.  Gene #71: '17q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
17Q LOSS MUTATED 84 67.8 (9.7)
17Q LOSS WILD-TYPE 420 63.1 (11.3)

Figure S65.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #2: 'AGE'

'17q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S66.  Gene #71: '17q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
17Q LOSS MUTATED 34 7 43
17Q LOSS WILD-TYPE 346 14 61

Figure S66.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S67.  Gene #72: '18p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
18P LOSS MUTATED 22 5 19
18P LOSS WILD-TYPE 358 16 85

Figure S67.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S68.  Gene #73: '18q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
18Q LOSS MUTATED 25 6 27
18Q LOSS WILD-TYPE 355 15 77

Figure S68.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p loss' versus 'Time to Death'

P value = 0.000485 (logrank test), Q value = 0.23

Table S69.  Gene #74: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 503 60 0.0 - 191.8 (22.8)
19P LOSS MUTATED 53 14 0.0 - 116.2 (18.8)
19P LOSS WILD-TYPE 450 46 0.1 - 191.8 (23.1)

Figure S69.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S70.  Gene #74: '19p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
19P LOSS MUTATED 17 4 33
19P LOSS WILD-TYPE 363 17 71

Figure S70.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q loss' versus 'Time to Death'

P value = 0.000444 (logrank test), Q value = 0.22

Table S71.  Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 503 60 0.0 - 191.8 (22.8)
19Q LOSS MUTATED 51 14 0.0 - 125.4 (18.8)
19Q LOSS WILD-TYPE 452 46 0.1 - 191.8 (23.0)

Figure S71.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S72.  Gene #75: '19q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
19Q LOSS MUTATED 17 4 31
19Q LOSS WILD-TYPE 363 17 73

Figure S72.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S73.  Gene #78: '21q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
21Q LOSS MUTATED 19 4 28
21Q LOSS WILD-TYPE 361 17 76

Figure S73.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'AGE'

P value = 4.87e-05 (Wilcoxon-test), Q value = 0.024

Table S74.  Gene #79: '22q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
22Q LOSS MUTATED 100 67.7 (8.9)
22Q LOSS WILD-TYPE 404 62.9 (11.5)

Figure S74.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #2: 'AGE'

'22q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S75.  Gene #79: '22q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
22Q LOSS MUTATED 41 10 49
22Q LOSS WILD-TYPE 339 11 55

Figure S75.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'xq loss' versus 'AGE'

P value = 0.000367 (Wilcoxon-test), Q value = 0.18

Table S76.  Gene #80: 'xq loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 504 63.8 (11.2)
XQ LOSS MUTATED 65 68.3 (9.6)
XQ LOSS WILD-TYPE 439 63.2 (11.3)

Figure S76.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #2: 'AGE'

'xq loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S77.  Gene #80: 'xq loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 380 21 104
XQ LOSS MUTATED 28 3 34
XQ LOSS WILD-TYPE 352 18 70

Figure S77.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 505

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 7

  • 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)