Correlation between copy number variations of arm-level result and selected clinical features
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1QZ28GK
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/C1QZ28GK
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 5 clinical features across 472 patients, 83 significant findings detected with Q value < 0.25.

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

  • 7q gain cnv correlated to 'Time to Death'.

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

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

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

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

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

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

  • 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 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 1p 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 'AGE' and '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 'AGE' and 'HISTOLOGICAL.TYPE'.

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

  • 12p loss cnv correlated to 'Time to Death' and '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 'AGE' and '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 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 83 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 37 (8%) 435 0.000752
(0.24) 		0.222
(1.00) 		6.06e-05
(0.0205) 		0.0903
(1.00) 		0.0164
(1.00)
13q gain 25 (5%) 447 0.853
(1.00) 		0.000502
(0.162) 		1.42e-06
(0.000502) 		0.657
(1.00) 		0.235
(1.00)
19p gain 44 (9%) 428 0.148
(1.00) 		2.8e-07
(0.000101) 		2.32e-07
(8.36e-05) 		0.293
(1.00) 		0.463
(1.00)
19q gain 47 (10%) 425 0.0548
(1.00) 		1.87e-08
(6.84e-06) 		4.51e-15
(1.75e-12) 		0.735
(1.00) 		0.627
(1.00)
20p gain 92 (19%) 380 0.00855
(1.00) 		7.46e-05
(0.0251) 		9.41e-14
(3.61e-11) 		0.00708
(1.00) 		0.0442
(1.00)
20q gain 108 (23%) 364 0.000792
(0.251) 		8.58e-06
(0.00297) 		9.29e-19
(3.65e-16) 		0.00774
(1.00) 		0.006
(1.00)
22q gain 29 (6%) 443 0.0516
(1.00) 		0.000667
(0.214) 		4.74e-10
(1.77e-07) 		0.676
(1.00) 		0.019
(1.00)
4p loss 82 (17%) 390 0.00849
(1.00) 		6.56e-05
(0.0221) 		5.21e-20
(2.06e-17) 		0.106
(1.00) 		0.388
(1.00)
4q loss 82 (17%) 390 0.0108
(1.00) 		8.22e-05
(0.0275) 		2.68e-19
(1.06e-16) 		0.106
(1.00) 		0.416
(1.00)
7p loss 38 (8%) 434 0.0292
(1.00) 		8.89e-05
(0.0297) 		6.29e-08
(2.28e-05) 		0.351
(1.00) 		0.301
(1.00)
7q loss 36 (8%) 436 0.395
(1.00) 		1.77e-05
(0.00604) 		5.91e-13
(2.26e-10) 		0.447
(1.00) 		0.285
(1.00)
8p loss 67 (14%) 405 0.0804
(1.00) 		1.61e-05
(0.00555) 		1.28e-25
(5.14e-23) 		0.773
(1.00) 		0.412
(1.00)
9p loss 87 (18%) 385 0.0261
(1.00) 		6.56e-06
(0.00228) 		4.17e-20
(1.65e-17) 		0.694
(1.00) 		0.0407
(1.00)
9q loss 103 (22%) 369 0.0105
(1.00) 		4.31e-10
(1.62e-07) 		2.28e-18
(8.94e-16) 		0.324
(1.00) 		0.152
(1.00)
11p loss 64 (14%) 408 0.00248
(0.767) 		0.000342
(0.112) 		1.68e-13
(6.43e-11) 		0.0364
(1.00) 		0.374
(1.00)
12p loss 36 (8%) 436 0.000324
(0.106) 		0.0807
(1.00) 		4.3e-08
(1.56e-05) 		0.252
(1.00) 		0.0494
(1.00)
12q loss 28 (6%) 444 0.000104
(0.0344) 		0.103
(1.00) 		2.4e-08
(8.78e-06) 		0.519
(1.00) 		0.502
(1.00)
14q loss 53 (11%) 419 0.016
(1.00) 		0.00048
(0.156) 		1.62e-11
(6.15e-09) 		0.42
(1.00) 		0.536
(1.00)
15q loss 91 (19%) 381 0.00492
(1.00) 		3.48e-06
(0.00122) 		9.28e-21
(3.68e-18) 		0.0721
(1.00) 		0.241
(1.00)
16p loss 81 (17%) 391 0.00918
(1.00) 		3.81e-05
(0.0129) 		1.27e-17
(4.98e-15) 		0.283
(1.00) 		0.00926
(1.00)
16q loss 118 (25%) 354 0.0582
(1.00) 		1.11e-06
(0.000394) 		9.75e-23
(3.88e-20) 		0.0777
(1.00) 		0.0105
(1.00)
17p loss 107 (23%) 365 0.00299
(0.913) 		1.3e-06
(0.000462) 		2.51e-25
(1e-22) 		0.398
(1.00) 		0.143
(1.00)
17q loss 77 (16%) 395 0.0651
(1.00) 		0.000165
(0.0546) 		1.25e-12
(4.76e-10) 		0.491
(1.00) 		0.468
(1.00)
19p loss 53 (11%) 419 0.000762
(0.242) 		0.0737
(1.00) 		3.11e-14
(1.2e-11) 		0.872
(1.00) 		0.111
(1.00)
19q loss 49 (10%) 423 0.000625
(0.201) 		0.159
(1.00) 		8.99e-12
(3.42e-09) 		0.404
(1.00) 		0.306
(1.00)
22q loss 92 (19%) 380 0.0105
(1.00) 		5.25e-06
(0.00184) 		5.47e-15
(2.12e-12) 		0.0392
(1.00) 		0.643
(1.00)
xq loss 63 (13%) 409 0.0104
(1.00) 		0.000222
(0.0732) 		4.15e-10
(1.56e-07) 		0.0365
(1.00) 		0.18
(1.00)
2p gain 79 (17%) 393 0.00455
(1.00) 		0.00898
(1.00) 		1.49e-08
(5.47e-06) 		0.223
(1.00) 		0.752
(1.00)
2q gain 63 (13%) 409 0.00287
(0.878) 		0.0946
(1.00) 		1.87e-05
(0.00639) 		0.294
(1.00) 		0.336
(1.00)
3q gain 66 (14%) 406 0.00263
(0.81) 		0.0168
(1.00) 		6.85e-09
(2.53e-06) 		0.464
(1.00) 		0.1
(1.00)
5p gain 45 (10%) 427 0.000975
(0.308) 		0.00898
(1.00) 		1.21e-09
(4.51e-07) 		0.118
(1.00) 		0.0879
(1.00)
6p gain 64 (14%) 408 0.878
(1.00) 		0.0689
(1.00) 		3.42e-07
(0.000122) 		0.554
(1.00) 		0.118
(1.00)
6q gain 53 (11%) 419 0.709
(1.00) 		0.15
(1.00) 		9.62e-05
(0.032) 		0.75
(1.00) 		0.07
(1.00)
7q gain 56 (12%) 416 0.00054
(0.174) 		0.567
(1.00) 		0.179
(1.00) 		0.155
(1.00) 		0.504
(1.00)
11p gain 18 (4%) 454 0.152
(1.00) 		0.0461
(1.00) 		0.000381
(0.124) 		1
(1.00) 		0.128
(1.00)
12p gain 56 (12%) 416 0.192
(1.00) 		0.911
(1.00) 		0.000278
(0.0916) 		0.27
(1.00) 		0.64
(1.00)
14q gain 35 (7%) 437 0.201
(1.00) 		0.201
(1.00) 		3.26e-06
(0.00115) 		0.00567
(1.00) 		0.181
(1.00)
17q gain 24 (5%) 448 0.00395
(1.00) 		0.0831
(1.00) 		0.000448
(0.145) 		1
(1.00) 		0.0114
(1.00)
18p gain 58 (12%) 414 0.0453
(1.00) 		0.00218
(0.678) 		2.43e-15
(9.45e-13) 		0.535
(1.00) 		0.00315
(0.958)
18q gain 36 (8%) 436 0.0223
(1.00) 		0.0912
(1.00) 		1.04e-06
(0.00037) 		0.704
(1.00) 		0.00898
(1.00)
21q gain 30 (6%) 442 0.174
(1.00) 		0.00386
(1.00) 		3.1e-07
(0.000111) 		0.403
(1.00) 		0.235
(1.00)
1p loss 21 (4%) 451 0.566
(1.00) 		0.0105
(1.00) 		3.71e-05
(0.0126) 		1
(1.00) 		0.00621
(1.00)
3p loss 45 (10%) 427 0.159
(1.00) 		0.00455
(1.00) 		1.47e-09
(5.45e-07) 		0.605
(1.00) 		0.952
(1.00)
3q loss 27 (6%) 445 0.682
(1.00) 		0.0532
(1.00) 		7.2e-06
(0.0025) 		0.279
(1.00) 		0.393
(1.00)
5p loss 46 (10%) 426 0.0039
(1.00) 		0.445
(1.00) 		2.74e-11
(1.04e-08) 		0.39
(1.00) 		0.019
(1.00)
5q loss 62 (13%) 410 0.00275
(0.844) 		0.00624
(1.00) 		2.36e-17
(9.21e-15) 		0.547
(1.00) 		0.322
(1.00)
6p loss 15 (3%) 457 0.665
(1.00) 		0.0464
(1.00) 		5.81e-06
(0.00203) 		0.772
(1.00) 		0.583
(1.00)
6q loss 21 (4%) 451 0.461
(1.00) 		0.0438
(1.00) 		1.74e-08
(6.39e-06) 		0.626
(1.00) 		0.439
(1.00)
8q loss 20 (4%) 452 0.79
(1.00) 		0.209
(1.00) 		1.34e-10
(5.07e-08) 		0.459
(1.00) 		0.34
(1.00)
10p loss 32 (7%) 440 0.115
(1.00) 		0.00234
(0.727) 		4.75e-09
(1.76e-06) 		0.426
(1.00) 		0.0431
(1.00)
10q loss 31 (7%) 441 0.27
(1.00) 		0.00459
(1.00) 		1.33e-06
(0.000469) 		0.306
(1.00) 		0.668
(1.00)
11q loss 60 (13%) 412 0.00439
(1.00) 		0.00118
(0.372) 		5.74e-14
(2.21e-11) 		0.00544
(1.00) 		0.146
(1.00)
13q loss 74 (16%) 398 0.00379
(1.00) 		0.00728
(1.00) 		8.9e-06
(0.00307) 		0.0935
(1.00) 		0.654
(1.00)
18p loss 43 (9%) 429 0.208
(1.00) 		0.0797
(1.00) 		1.64e-05
(0.00564) 		0.29
(1.00) 		0.282
(1.00)
18q loss 54 (11%) 418 0.247
(1.00) 		0.0311
(1.00) 		2.69e-08
(9.78e-06) 		0.337
(1.00) 		0.269
(1.00)
21q loss 46 (10%) 426 0.0129
(1.00) 		0.00975
(1.00) 		4.05e-09
(1.5e-06) 		1
(1.00) 		0.176
(1.00)
1q gain 162 (34%) 310 0.213
(1.00) 		0.0187
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.848
(1.00)
3p gain 36 (8%) 436 0.0608
(1.00) 		0.3
(1.00) 		0.0341
(1.00) 		0.0534
(1.00) 		0.225
(1.00)
4p gain 12 (3%) 460 0.423
(1.00) 		0.112
(1.00) 		0.00143
(0.45) 		0.749
(1.00) 		0.0964
(1.00)
4q gain 8 (2%) 464 0.608
(1.00) 		0.692
(1.00) 		0.0154
(1.00) 		0.449
(1.00) 		0.515
(1.00)
5q gain 17 (4%) 455 0.119
(1.00) 		0.565
(1.00) 		0.00748
(1.00) 		0.417
(1.00) 		0.232
(1.00)
7p gain 58 (12%) 414 0.0143
(1.00) 		0.401
(1.00) 		0.0799
(1.00) 		0.352
(1.00) 		0.722
(1.00)
8p gain 105 (22%) 367 0.0851
(1.00) 		0.0252
(1.00) 		0.864
(1.00) 		0.0509
(1.00) 		0.0893
(1.00)
8q gain 135 (29%) 337 0.0132
(1.00) 		0.336
(1.00) 		0.0157
(1.00) 		0.0558
(1.00) 		0.146
(1.00)
9p gain 17 (4%) 455 0.432
(1.00) 		0.856
(1.00) 		0.376
(1.00) 		0.417
(1.00) 		0.253
(1.00)
9q gain 7 (1%) 465 0.715
(1.00) 		0.854
(1.00) 		0.19
(1.00) 		0.679
(1.00) 		0.204
(1.00)
10p gain 106 (22%) 366 0.955
(1.00) 		0.385
(1.00) 		0.864
(1.00) 		0.465
(1.00) 		0.843
(1.00)
10q gain 100 (21%) 372 0.489
(1.00) 		0.884
(1.00) 		0.926
(1.00) 		0.618
(1.00) 		0.326
(1.00)
11q gain 16 (3%) 456 0.00525
(1.00) 		0.136
(1.00) 		0.0733
(1.00) 		1
(1.00) 		0.236
(1.00)
12q gain 44 (9%) 428 0.186
(1.00) 		0.357
(1.00) 		0.183
(1.00) 		0.293
(1.00) 		0.804
(1.00)
15q gain 9 (2%) 463 0.00874
(1.00) 		0.998
(1.00) 		0.586
(1.00) 		0.457
(1.00) 		0.0763
(1.00)
16p gain 20 (4%) 452 0.653
(1.00) 		0.0628
(1.00) 		0.125
(1.00) 		0.212
(1.00) 		0.0893
(1.00)
16q gain 10 (2%) 462 0.885
(1.00) 		0.0792
(1.00) 		0.193
(1.00) 		0.294
(1.00) 		0.00199
(0.621)
17p gain 10 (2%) 462 0.787
(1.00) 		0.547
(1.00) 		0.254
(1.00) 		1
(1.00) 		0.172
(1.00)
xq gain 54 (11%) 418 0.0317
(1.00) 		0.484
(1.00) 		0.881
(1.00) 		0.523
(1.00) 		0.139
(1.00)
1q loss 13 (3%) 459 0.0789
(1.00) 		0.0631
(1.00) 		0.00662
(1.00) 		0.366
(1.00) 		0.0129
(1.00)
2p loss 10 (2%) 462 0.0186
(1.00) 		0.0543
(1.00) 		0.627
(1.00) 		0.0693
(1.00) 		0.101
(1.00)
2q loss 16 (3%) 456 0.00166
(0.518) 		0.0278
(1.00) 		0.422
(1.00) 		0.0487
(1.00) 		0.34
(1.00)
20p loss 16 (3%) 456 0.567
(1.00) 		0.0808
(1.00) 		0.00771
(1.00) 		0.172
(1.00) 		0.14
(1.00)
20q loss 9 (2%) 463 0.247
(1.00) 		0.432
(1.00) 		0.00458
(1.00) 		0.127
(1.00) 		1
(1.00)
'1p gain' versus 'Time to Death'

P value = 0.000752 (logrank test), Q value = 0.24

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

nPatients nDeath Duration Range (Median), Month
ALL 469 57 0.0 - 191.8 (20.9)
1P GAIN MUTATED 37 9 0.0 - 72.6 (11.5)
1P GAIN WILD-TYPE 432 48 0.1 - 191.8 (23.1)

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

'1p gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.02

Table S2.  Gene #1: '1p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
1P GAIN MUTATED 17 2 18
1P GAIN WILD-TYPE 343 17 75

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'2p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.49e-08 (Fisher's exact test), Q value = 5.5e-06

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
2P GAIN MUTATED 39 5 35
2P GAIN WILD-TYPE 321 14 58

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

'2q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.0064

Table S4.  Gene #4: '2q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
2Q GAIN MUTATED 33 4 26
2Q GAIN WILD-TYPE 327 15 67

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3q gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.85e-09 (Fisher's exact test), Q value = 2.5e-06

Table S5.  Gene #6: '3q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
3Q GAIN MUTATED 30 4 32
3Q GAIN WILD-TYPE 330 15 61

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.21e-09 (Fisher's exact test), Q value = 4.5e-07

Table S6.  Gene #9: '5p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
5P GAIN MUTATED 16 3 26
5P GAIN WILD-TYPE 344 16 67

Figure S6.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6p gain' versus 'HISTOLOGICAL.TYPE'

P value = 3.42e-07 (Fisher's exact test), Q value = 0.00012

Table S7.  Gene #11: '6p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
6P GAIN MUTATED 33 1 30
6P GAIN WILD-TYPE 327 18 63

Figure S7.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6q gain' versus 'HISTOLOGICAL.TYPE'

P value = 9.62e-05 (Fisher's exact test), Q value = 0.032

Table S8.  Gene #12: '6q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
6Q GAIN MUTATED 29 1 23
6Q GAIN WILD-TYPE 331 18 70

Figure S8.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q gain' versus 'Time to Death'

P value = 0.00054 (logrank test), Q value = 0.17

Table S9.  Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 469 57 0.0 - 191.8 (20.9)
7Q GAIN MUTATED 55 13 0.0 - 125.4 (15.4)
7Q GAIN WILD-TYPE 414 44 0.1 - 191.8 (23.1)

Figure S9.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000381 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #21: '11p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
11P GAIN MUTATED 7 0 11
11P GAIN WILD-TYPE 353 19 82

Figure S10.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000278 (Fisher's exact test), Q value = 0.092

Table S11.  Gene #23: '12p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
12P GAIN MUTATED 31 2 23
12P GAIN WILD-TYPE 329 17 70

Figure S11.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q gain' versus 'AGE'

P value = 0.000502 (t-test), Q value = 0.16

Table S12.  Gene #25: '13q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
13Q GAIN MUTATED 25 69.0 (6.5)
13Q GAIN WILD-TYPE 446 63.5 (11.4)

Figure S12.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #2: 'AGE'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.42e-06 (Fisher's exact test), Q value = 5e-04

Table S13.  Gene #25: '13q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
13Q GAIN MUTATED 8 1 16
13Q GAIN WILD-TYPE 352 18 77

Figure S13.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q gain' versus 'HISTOLOGICAL.TYPE'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0011

Table S14.  Gene #26: '14q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
14Q GAIN MUTATED 14 2 19
14Q GAIN WILD-TYPE 346 17 74

Figure S14.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000448 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #31: '17q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
17Q GAIN MUTATED 11 0 13
17Q GAIN WILD-TYPE 349 19 80

Figure S15.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18p gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.43e-15 (Fisher's exact test), Q value = 9.5e-13

Table S16.  Gene #32: '18p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
18P GAIN MUTATED 18 4 36
18P GAIN WILD-TYPE 342 15 57

Figure S16.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00037

Table S17.  Gene #33: '18q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
18Q GAIN MUTATED 14 3 19
18Q GAIN WILD-TYPE 346 16 74

Figure S17.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p gain' versus 'AGE'

P value = 2.8e-07 (t-test), Q value = 1e-04

Table S18.  Gene #34: '19p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
19P GAIN MUTATED 44 71.1 (8.5)
19P GAIN WILD-TYPE 427 63.0 (11.3)

Figure S18.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'AGE'

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.32e-07 (Fisher's exact test), Q value = 8.4e-05

Table S19.  Gene #34: '19p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
19P GAIN MUTATED 18 3 23
19P GAIN WILD-TYPE 342 16 70

Figure S19.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q gain' versus 'AGE'

P value = 1.87e-08 (t-test), Q value = 6.8e-06

Table S20.  Gene #35: '19q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
19Q GAIN MUTATED 47 71.7 (8.6)
19Q GAIN WILD-TYPE 424 62.9 (11.2)

Figure S20.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'AGE'

'19q gain' versus 'HISTOLOGICAL.TYPE'

P value = 4.51e-15 (Fisher's exact test), Q value = 1.7e-12

Table S21.  Gene #35: '19q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
19Q GAIN MUTATED 12 3 32
19Q GAIN WILD-TYPE 348 16 61

Figure S21.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'AGE'

P value = 7.46e-05 (t-test), Q value = 0.025

Table S22.  Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
20P GAIN MUTATED 92 67.8 (10.3)
20P GAIN WILD-TYPE 379 62.8 (11.3)

Figure S22.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 9.41e-14 (Fisher's exact test), Q value = 3.6e-11

Table S23.  Gene #36: '20p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
20P GAIN MUTATED 42 4 46
20P GAIN WILD-TYPE 318 15 47

Figure S23.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'AGE'

P value = 8.58e-06 (t-test), Q value = 0.003

Table S24.  Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
20Q GAIN MUTATED 108 67.8 (10.1)
20Q GAIN WILD-TYPE 363 62.6 (11.3)

Figure S24.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 9.29e-19 (Fisher's exact test), Q value = 3.7e-16

Table S25.  Gene #37: '20q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
20Q GAIN MUTATED 48 4 56
20Q GAIN WILD-TYPE 312 15 37

Figure S25.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 3.1e-07 (Fisher's exact test), Q value = 0.00011

Table S26.  Gene #38: '21q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
21Q GAIN MUTATED 11 0 19
21Q GAIN WILD-TYPE 349 19 74

Figure S26.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q gain' versus 'AGE'

P value = 0.000667 (t-test), Q value = 0.21

Table S27.  Gene #39: '22q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
22Q GAIN MUTATED 28 69.7 (8.4)
22Q GAIN WILD-TYPE 443 63.4 (11.3)

Figure S27.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'AGE'

'22q gain' versus 'HISTOLOGICAL.TYPE'

P value = 4.74e-10 (Fisher's exact test), Q value = 1.8e-07

Table S28.  Gene #39: '22q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
22Q GAIN MUTATED 7 1 21
22Q GAIN WILD-TYPE 353 18 72

Figure S28.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'1p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.71e-05 (Fisher's exact test), Q value = 0.013

Table S29.  Gene #41: '1p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
1P LOSS MUTATED 7 2 12
1P LOSS WILD-TYPE 353 17 81

Figure S29.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.47e-09 (Fisher's exact test), Q value = 5.5e-07

Table S30.  Gene #45: '3p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
3P LOSS MUTATED 16 6 23
3P LOSS WILD-TYPE 344 13 70

Figure S30.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.2e-06 (Fisher's exact test), Q value = 0.0025

Table S31.  Gene #46: '3q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
3Q LOSS MUTATED 10 1 16
3Q LOSS WILD-TYPE 350 18 77

Figure S31.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4p loss' versus 'AGE'

P value = 6.56e-05 (t-test), Q value = 0.022

Table S32.  Gene #47: '4p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
4P LOSS MUTATED 82 68.0 (9.9)
4P LOSS WILD-TYPE 389 62.9 (11.4)

Figure S32.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'AGE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.21e-20 (Fisher's exact test), Q value = 2.1e-17

Table S33.  Gene #47: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
4P LOSS MUTATED 29 4 49
4P LOSS WILD-TYPE 331 15 44

Figure S33.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'AGE'

P value = 8.22e-05 (t-test), Q value = 0.028

Table S34.  Gene #48: '4q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
4Q LOSS MUTATED 82 68.0 (10.0)
4Q LOSS WILD-TYPE 389 62.9 (11.3)

Figure S34.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #2: 'AGE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.68e-19 (Fisher's exact test), Q value = 1.1e-16

Table S35.  Gene #48: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
4Q LOSS MUTATED 29 5 48
4Q LOSS WILD-TYPE 331 14 45

Figure S35.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.74e-11 (Fisher's exact test), Q value = 1e-08

Table S36.  Gene #49: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
5P LOSS MUTATED 16 1 29
5P LOSS WILD-TYPE 344 18 64

Figure S36.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.36e-17 (Fisher's exact test), Q value = 9.2e-15

Table S37.  Gene #50: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
5Q LOSS MUTATED 19 3 40
5Q LOSS WILD-TYPE 341 16 53

Figure S37.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.81e-06 (Fisher's exact test), Q value = 0.002

Table S38.  Gene #51: '6p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
6P LOSS MUTATED 3 1 11
6P LOSS WILD-TYPE 357 18 82

Figure S38.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.74e-08 (Fisher's exact test), Q value = 6.4e-06

Table S39.  Gene #52: '6q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
6Q LOSS MUTATED 4 1 16
6Q LOSS WILD-TYPE 356 18 77

Figure S39.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7p loss' versus 'AGE'

P value = 8.89e-05 (t-test), Q value = 0.03

Table S40.  Gene #53: '7p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
7P LOSS MUTATED 38 70.4 (9.8)
7P LOSS WILD-TYPE 433 63.2 (11.2)

Figure S40.  Get High-res Image Gene #53: '7p loss' versus Clinical Feature #2: 'AGE'

'7p loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.29e-08 (Fisher's exact test), Q value = 2.3e-05

Table S41.  Gene #53: '7p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
7P LOSS MUTATED 14 2 22
7P LOSS WILD-TYPE 346 17 71

Figure S41.  Get High-res Image Gene #53: '7p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss' versus 'AGE'

P value = 1.77e-05 (t-test), Q value = 0.006

Table S42.  Gene #54: '7q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
7Q LOSS MUTATED 36 69.5 (7.1)
7Q LOSS WILD-TYPE 435 63.3 (11.4)

Figure S42.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #2: 'AGE'

'7q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.91e-13 (Fisher's exact test), Q value = 2.3e-10

Table S43.  Gene #54: '7q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
7Q LOSS MUTATED 8 2 26
7Q LOSS WILD-TYPE 352 17 67

Figure S43.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss' versus 'AGE'

P value = 1.61e-05 (t-test), Q value = 0.0056

Table S44.  Gene #55: '8p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
8P LOSS MUTATED 67 68.5 (8.8)
8P LOSS WILD-TYPE 404 63.0 (11.5)

Figure S44.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #2: 'AGE'

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.28e-25 (Fisher's exact test), Q value = 5.1e-23

Table S45.  Gene #55: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
8P LOSS MUTATED 15 4 48
8P LOSS WILD-TYPE 345 15 45

Figure S45.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.34e-10 (Fisher's exact test), Q value = 5.1e-08

Table S46.  Gene #56: '8q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
8Q LOSS MUTATED 2 1 17
8Q LOSS WILD-TYPE 358 18 76

Figure S46.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'AGE'

P value = 6.56e-06 (t-test), Q value = 0.0023

Table S47.  Gene #57: '9p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
9P LOSS MUTATED 87 68.0 (8.6)
9P LOSS WILD-TYPE 384 62.8 (11.6)

Figure S47.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'AGE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.17e-20 (Fisher's exact test), Q value = 1.7e-17

Table S48.  Gene #57: '9p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
9P LOSS MUTATED 31 7 49
9P LOSS WILD-TYPE 329 12 44

Figure S48.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss' versus 'AGE'

P value = 4.31e-10 (t-test), Q value = 1.6e-07

Table S49.  Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
9Q LOSS MUTATED 103 69.2 (8.9)
9Q LOSS WILD-TYPE 368 62.3 (11.4)

Figure S49.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

'9q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.28e-18 (Fisher's exact test), Q value = 8.9e-16

Table S50.  Gene #58: '9q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
9Q LOSS MUTATED 43 8 52
9Q LOSS WILD-TYPE 317 11 41

Figure S50.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.75e-09 (Fisher's exact test), Q value = 1.8e-06

Table S51.  Gene #59: '10p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
10P LOSS MUTATED 9 3 20
10P LOSS WILD-TYPE 351 16 73

Figure S51.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00047

Table S52.  Gene #60: '10q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
10Q LOSS MUTATED 11 3 17
10Q LOSS WILD-TYPE 349 16 76

Figure S52.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p loss' versus 'AGE'

P value = 0.000342 (t-test), Q value = 0.11

Table S53.  Gene #61: '11p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
11P LOSS MUTATED 64 68.2 (10.1)
11P LOSS WILD-TYPE 407 63.1 (11.3)

Figure S53.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #2: 'AGE'

'11p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.68e-13 (Fisher's exact test), Q value = 6.4e-11

Table S54.  Gene #61: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
11P LOSS MUTATED 23 6 35
11P LOSS WILD-TYPE 337 13 58

Figure S54.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.74e-14 (Fisher's exact test), Q value = 2.2e-11

Table S55.  Gene #62: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
11Q LOSS MUTATED 20 7 33
11Q LOSS WILD-TYPE 340 12 60

Figure S55.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p loss' versus 'Time to Death'

P value = 0.000324 (logrank test), Q value = 0.11

Table S56.  Gene #63: '12p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 469 57 0.0 - 191.8 (20.9)
12P LOSS MUTATED 36 11 0.1 - 102.0 (19.3)
12P LOSS WILD-TYPE 433 46 0.0 - 191.8 (21.2)

Figure S56.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #1: 'Time to Death'

'12p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.3e-08 (Fisher's exact test), Q value = 1.6e-05

Table S57.  Gene #63: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
12P LOSS MUTATED 13 1 22
12P LOSS WILD-TYPE 347 18 71

Figure S57.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12q loss' versus 'Time to Death'

P value = 0.000104 (logrank test), Q value = 0.034

Table S58.  Gene #64: '12q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 469 57 0.0 - 191.8 (20.9)
12Q LOSS MUTATED 28 9 0.8 - 97.7 (18.5)
12Q LOSS WILD-TYPE 441 48 0.0 - 191.8 (21.7)

Figure S58.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #1: 'Time to Death'

'12q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.4e-08 (Fisher's exact test), Q value = 8.8e-06

Table S59.  Gene #64: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
12Q LOSS MUTATED 8 1 19
12Q LOSS WILD-TYPE 352 18 74

Figure S59.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.9e-06 (Fisher's exact test), Q value = 0.0031

Table S60.  Gene #65: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
13Q LOSS MUTATED 40 4 30
13Q LOSS WILD-TYPE 320 15 63

Figure S60.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'AGE'

P value = 0.00048 (t-test), Q value = 0.16

Table S61.  Gene #66: '14q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
14Q LOSS MUTATED 53 68.0 (8.6)
14Q LOSS WILD-TYPE 418 63.3 (11.5)

Figure S61.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #2: 'AGE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.62e-11 (Fisher's exact test), Q value = 6.2e-09

Table S62.  Gene #66: '14q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
14Q LOSS MUTATED 19 3 31
14Q LOSS WILD-TYPE 341 16 62

Figure S62.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss' versus 'AGE'

P value = 3.48e-06 (t-test), Q value = 0.0012

Table S63.  Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
15Q LOSS MUTATED 91 68.6 (10.5)
15Q LOSS WILD-TYPE 380 62.6 (11.2)

Figure S63.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

'15q loss' versus 'HISTOLOGICAL.TYPE'

P value = 9.28e-21 (Fisher's exact test), Q value = 3.7e-18

Table S64.  Gene #67: '15q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
15Q LOSS MUTATED 33 7 51
15Q LOSS WILD-TYPE 327 12 42

Figure S64.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss' versus 'AGE'

P value = 3.81e-05 (t-test), Q value = 0.013

Table S65.  Gene #68: '16p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
16P LOSS MUTATED 81 68.2 (10.0)
16P LOSS WILD-TYPE 390 62.9 (11.3)

Figure S65.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #2: 'AGE'

'16p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.27e-17 (Fisher's exact test), Q value = 5e-15

Table S66.  Gene #68: '16p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
16P LOSS MUTATED 30 5 46
16P LOSS WILD-TYPE 330 14 47

Figure S66.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'AGE'

P value = 1.11e-06 (t-test), Q value = 0.00039

Table S67.  Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
16Q LOSS MUTATED 118 67.8 (9.6)
16Q LOSS WILD-TYPE 353 62.4 (11.5)

Figure S67.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 9.75e-23 (Fisher's exact test), Q value = 3.9e-20

Table S68.  Gene #69: '16q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
16Q LOSS MUTATED 50 6 62
16Q LOSS WILD-TYPE 310 13 31

Figure S68.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'AGE'

P value = 1.3e-06 (t-test), Q value = 0.00046

Table S69.  Gene #70: '17p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
17P LOSS MUTATED 107 68.0 (9.3)
17P LOSS WILD-TYPE 364 62.6 (11.5)

Figure S69.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #2: 'AGE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.51e-25 (Fisher's exact test), Q value = 1e-22

Table S70.  Gene #70: '17p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
17P LOSS MUTATED 39 9 59
17P LOSS WILD-TYPE 321 10 34

Figure S70.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss' versus 'AGE'

P value = 0.000165 (t-test), Q value = 0.055

Table S71.  Gene #71: '17q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
17Q LOSS MUTATED 77 67.9 (10.0)
17Q LOSS WILD-TYPE 394 63.0 (11.4)

Figure S71.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #2: 'AGE'

'17q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.25e-12 (Fisher's exact test), Q value = 4.8e-10

Table S72.  Gene #71: '17q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
17Q LOSS MUTATED 32 7 38
17Q LOSS WILD-TYPE 328 12 55

Figure S72.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0056

Table S73.  Gene #72: '18p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
18P LOSS MUTATED 20 5 18
18P LOSS WILD-TYPE 340 14 75

Figure S73.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.69e-08 (Fisher's exact test), Q value = 9.8e-06

Table S74.  Gene #73: '18q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
18Q LOSS MUTATED 23 6 25
18Q LOSS WILD-TYPE 337 13 68

Figure S74.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p loss' versus 'Time to Death'

P value = 0.000762 (logrank test), Q value = 0.24

Table S75.  Gene #74: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 469 57 0.0 - 191.8 (20.9)
19P LOSS MUTATED 52 13 0.0 - 97.1 (15.6)
19P LOSS WILD-TYPE 417 44 0.1 - 191.8 (22.5)

Figure S75.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.11e-14 (Fisher's exact test), Q value = 1.2e-11

Table S76.  Gene #74: '19p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
19P LOSS MUTATED 16 4 33
19P LOSS WILD-TYPE 344 15 60

Figure S76.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q loss' versus 'Time to Death'

P value = 0.000625 (logrank test), Q value = 0.2

Table S77.  Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 469 57 0.0 - 191.8 (20.9)
19Q LOSS MUTATED 48 13 0.0 - 125.4 (14.9)
19Q LOSS WILD-TYPE 421 44 0.1 - 191.8 (22.0)

Figure S77.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.99e-12 (Fisher's exact test), Q value = 3.4e-09

Table S78.  Gene #75: '19q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
19Q LOSS MUTATED 16 4 29
19Q LOSS WILD-TYPE 344 15 64

Figure S78.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.05e-09 (Fisher's exact test), Q value = 1.5e-06

Table S79.  Gene #78: '21q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
21Q LOSS MUTATED 17 4 25
21Q LOSS WILD-TYPE 343 15 68

Figure S79.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'AGE'

P value = 5.25e-06 (t-test), Q value = 0.0018

Table S80.  Gene #79: '22q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
22Q LOSS MUTATED 92 68.0 (9.2)
22Q LOSS WILD-TYPE 379 62.8 (11.5)

Figure S80.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #2: 'AGE'

'22q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.47e-15 (Fisher's exact test), Q value = 2.1e-12

Table S81.  Gene #79: '22q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
22Q LOSS MUTATED 39 9 44
22Q LOSS WILD-TYPE 321 10 49

Figure S81.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'xq loss' versus 'AGE'

P value = 0.000222 (t-test), Q value = 0.073

Table S82.  Gene #80: 'xq loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 471 63.8 (11.3)
XQ LOSS MUTATED 63 68.3 (9.9)
XQ LOSS WILD-TYPE 408 63.1 (11.3)

Figure S82.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #2: 'AGE'

'xq loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.15e-10 (Fisher's exact test), Q value = 1.6e-07

Table S83.  Gene #80: 'xq loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 360 19 93
XQ LOSS MUTATED 27 3 33
XQ LOSS WILD-TYPE 333 16 60

Figure S83.  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 = 472

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 5

  • 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

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] 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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