Correlation between copy number variations of arm-level result and selected clinical features
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1TH8KCP
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/C1TH8KCP
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 474 patients, 83 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 'Time to Death' and 'HISTOLOGICAL.TYPE'.

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

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

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

  • 11q gain cnv correlated to 'Time to Death'.

  • 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 'Time to Death',  '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 '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
20q gain 108 (23%) 366 0.0005
(0.16) 		7.26e-06
(0.00253) 		6.91e-19
(2.72e-16) 		0.0105
(1.00) 		0.00563
(1.00)
5p gain 45 (9%) 429 0.000213
(0.0698) 		0.00852
(1.00) 		1.11e-09
(4.14e-07) 		0.118
(1.00) 		0.0864
(1.00)
13q gain 25 (5%) 449 0.73
(1.00) 		0.000466
(0.15) 		1.35e-06
(0.000477) 		0.655
(1.00) 		0.233
(1.00)
19p gain 43 (9%) 431 0.168
(1.00) 		3.22e-07
(0.000116) 		5.04e-07
(0.000181) 		0.291
(1.00) 		0.461
(1.00)
19q gain 46 (10%) 428 0.0643
(1.00) 		2.03e-08
(7.43e-06) 		1.71e-14
(6.62e-12) 		0.864
(1.00) 		0.625
(1.00)
20p gain 92 (19%) 382 0.00466
(1.00) 		6.52e-05
(0.0219) 		8.24e-14
(3.17e-11) 		0.00974
(1.00) 		0.0414
(1.00)
22q gain 29 (6%) 445 0.0597
(1.00) 		0.000581
(0.185) 		4.42e-10
(1.66e-07) 		0.676
(1.00) 		0.0185
(1.00)
4p loss 82 (17%) 392 0.0125
(1.00) 		5.82e-05
(0.0196) 		4.26e-20
(1.69e-17) 		0.106
(1.00) 		0.378
(1.00)
4q loss 82 (17%) 392 0.00557
(1.00) 		7.32e-05
(0.0245) 		2.23e-19
(8.78e-17) 		0.106
(1.00) 		0.407
(1.00)
7p loss 38 (8%) 436 0.0352
(1.00) 		8.28e-05
(0.0277) 		5.85e-08
(2.12e-05) 		0.351
(1.00) 		0.286
(1.00)
7q loss 36 (8%) 438 0.427
(1.00) 		1.45e-05
(0.00496) 		5.39e-13
(2.06e-10) 		0.447
(1.00) 		0.276
(1.00)
8p loss 67 (14%) 407 0.0959
(1.00) 		1.33e-05
(0.00455) 		1.03e-25
(4.12e-23) 		0.884
(1.00) 		0.394
(1.00)
9p loss 85 (18%) 389 0.0121
(1.00) 		7.27e-06
(0.00253) 		7.1e-20
(2.8e-17) 		0.598
(1.00) 		0.0277
(1.00)
9q loss 102 (22%) 372 0.0142
(1.00) 		3.47e-10
(1.31e-07) 		9.68e-19
(3.79e-16) 		0.265
(1.00) 		0.137
(1.00)
11p loss 64 (14%) 410 0.00404
(1.00) 		0.000312
(0.102) 		1.49e-13
(5.71e-11) 		0.0365
(1.00) 		0.363
(1.00)
12p loss 36 (8%) 438 0.00062
(0.197) 		0.0764
(1.00) 		4.01e-08
(1.46e-05) 		0.252
(1.00) 		0.0472
(1.00)
12q loss 28 (6%) 446 0.000151
(0.0501) 		0.0969
(1.00) 		2.26e-08
(8.25e-06) 		0.519
(1.00) 		0.5
(1.00)
15q loss 91 (19%) 383 0.00293
(0.897) 		3.03e-06
(0.00106) 		7.41e-21
(2.94e-18) 		0.0925
(1.00) 		0.232
(1.00)
16p loss 81 (17%) 393 0.0138
(1.00) 		4.29e-05
(0.0146) 		8.85e-19
(3.47e-16) 		0.344
(1.00) 		0.00669
(1.00)
16q loss 117 (25%) 357 0.0381
(1.00) 		8.12e-07
(0.000291) 		3.38e-23
(1.35e-20) 		0.0984
(1.00) 		0.00801
(1.00)
17p loss 107 (23%) 367 0.00188
(0.584) 		1.14e-06
(0.000404) 		1.91e-25
(7.61e-23) 		0.465
(1.00) 		0.134
(1.00)
17q loss 77 (16%) 397 0.0363
(1.00) 		0.000154
(0.0511) 		1.06e-12
(4.02e-10) 		0.491
(1.00) 		0.458
(1.00)
19p loss 53 (11%) 421 0.000199
(0.0651) 		0.0678
(1.00) 		2.53e-14
(9.75e-12) 		0.872
(1.00) 		0.107
(1.00)
19q loss 50 (11%) 424 0.000155
(0.0511) 		0.137
(1.00) 		2.32e-12
(8.81e-10) 		0.323
(1.00) 		0.3
(1.00)
22q loss 91 (19%) 383 0.0168
(1.00) 		9.82e-06
(0.00339) 		2.02e-14
(7.81e-12) 		0.052
(1.00) 		0.588
(1.00)
xq loss 62 (13%) 412 0.0135
(1.00) 		0.00036
(0.117) 		1.48e-09
(5.49e-07) 		0.0496
(1.00) 		0.165
(1.00)
1p gain 38 (8%) 436 0.00139
(0.435) 		0.116
(1.00) 		1.61e-05
(0.00549) 		0.0905
(1.00) 		0.0183
(1.00)
2p gain 81 (17%) 393 0.00403
(1.00) 		0.00593
(1.00) 		8.21e-09
(3.03e-06) 		0.344
(1.00) 		0.463
(1.00)
2q gain 65 (14%) 409 0.0022
(0.677) 		0.0692
(1.00) 		1e-05
(0.00345) 		0.375
(1.00) 		0.165
(1.00)
3q gain 65 (14%) 409 0.0041
(1.00) 		0.0139
(1.00) 		1.82e-08
(6.69e-06) 		0.554
(1.00) 		0.0955
(1.00)
6p gain 65 (14%) 409 0.962
(1.00) 		0.0591
(1.00) 		5.58e-07
(2e-04) 		0.554
(1.00) 		0.131
(1.00)
6q gain 54 (11%) 420 0.644
(1.00) 		0.132
(1.00) 		0.000129
(0.0431) 		0.873
(1.00) 		0.0825
(1.00)
11p gain 18 (4%) 456 0.0363
(1.00) 		0.0446
(1.00) 		0.000312
(0.102) 		1
(1.00) 		0.126
(1.00)
11q gain 16 (3%) 458 0.000437
(0.141) 		0.132
(1.00) 		0.0617
(1.00) 		1
(1.00) 		0.233
(1.00)
12p gain 55 (12%) 419 0.19
(1.00) 		0.932
(1.00) 		0.000154
(0.0511) 		0.155
(1.00) 		0.697
(1.00)
14q gain 35 (7%) 439 0.278
(1.00) 		0.199
(1.00) 		3.11e-06
(0.00109) 		0.00568
(1.00) 		0.179
(1.00)
17q gain 24 (5%) 450 0.00725
(1.00) 		0.0801
(1.00) 		0.000431
(0.139) 		1
(1.00) 		0.0111
(1.00)
18p gain 58 (12%) 416 0.0252
(1.00) 		0.00211
(0.652) 		2.14e-15
(8.32e-13) 		0.535
(1.00) 		0.00308
(0.94)
18q gain 36 (8%) 438 0.00787
(1.00) 		0.0917
(1.00) 		9.71e-07
(0.000346) 		0.705
(1.00) 		0.00868
(1.00)
21q gain 29 (6%) 445 0.0462
(1.00) 		0.0046
(1.00) 		8.57e-07
(0.000306) 		0.401
(1.00) 		0.199
(1.00)
1p loss 19 (4%) 455 0.581
(1.00) 		0.0385
(1.00) 		5.11e-05
(0.0173) 		0.797
(1.00) 		0.00369
(1.00)
3p loss 45 (9%) 429 0.179
(1.00) 		0.00419
(1.00) 		1.34e-09
(4.98e-07) 		0.605
(1.00) 		0.952
(1.00)
3q loss 28 (6%) 446 0.713
(1.00) 		0.0594
(1.00) 		1.85e-06
(0.000651) 		0.28
(1.00) 		0.39
(1.00)
5p loss 46 (10%) 428 0.00761
(1.00) 		0.439
(1.00) 		2.51e-11
(9.5e-09) 		0.308
(1.00) 		0.0185
(1.00)
5q loss 62 (13%) 412 0.0052
(1.00) 		0.00604
(1.00) 		2.21e-17
(8.63e-15) 		0.546
(1.00) 		0.32
(1.00)
6p loss 15 (3%) 459 0.653
(1.00) 		0.0449
(1.00) 		5.58e-06
(0.00195) 		0.772
(1.00) 		0.58
(1.00)
6q loss 21 (4%) 453 0.516
(1.00) 		0.0422
(1.00) 		1.65e-08
(6.07e-06) 		0.625
(1.00) 		0.462
(1.00)
8q loss 20 (4%) 454 0.768
(1.00) 		0.197
(1.00) 		1.26e-10
(4.77e-08) 		0.459
(1.00) 		0.337
(1.00)
10p loss 32 (7%) 442 0.128
(1.00) 		0.0022
(0.677) 		4.42e-09
(1.63e-06) 		0.543
(1.00) 		0.0422
(1.00)
10q loss 31 (7%) 443 0.292
(1.00) 		0.00408
(1.00) 		1.25e-06
(0.000443) 		0.306
(1.00) 		0.666
(1.00)
11q loss 60 (13%) 414 0.00689
(1.00) 		0.00105
(0.33) 		5.07e-14
(1.95e-11) 		0.00543
(1.00) 		0.139
(1.00)
13q loss 74 (16%) 400 0.0062
(1.00) 		0.00699
(1.00) 		7.44e-06
(0.00258) 		0.0941
(1.00) 		0.653
(1.00)
14q loss 50 (11%) 424 0.0413
(1.00) 		0.000997
(0.315) 		7.47e-10
(2.8e-07) 		0.408
(1.00) 		0.45
(1.00)
18p loss 43 (9%) 431 0.23
(1.00) 		0.0762
(1.00) 		1.45e-05
(0.00496) 		0.291
(1.00) 		0.275
(1.00)
18q loss 54 (11%) 420 0.275
(1.00) 		0.0292
(1.00) 		2.3e-08
(8.39e-06) 		0.338
(1.00) 		0.264
(1.00)
21q loss 47 (10%) 427 0.0228
(1.00) 		0.00788
(1.00) 		1.21e-09
(4.51e-07) 		1
(1.00) 		0.199
(1.00)
1q gain 164 (35%) 310 0.132
(1.00) 		0.0107
(1.00) 		0.813
(1.00) 		0.915
(1.00) 		0.939
(1.00)
3p gain 37 (8%) 437 0.111
(1.00) 		0.289
(1.00) 		0.0141
(1.00) 		0.037
(1.00) 		0.174
(1.00)
4p gain 12 (3%) 462 0.0919
(1.00) 		0.11
(1.00) 		0.0014
(0.436) 		0.748
(1.00) 		0.0951
(1.00)
4q gain 8 (2%) 466 0.637
(1.00) 		0.686
(1.00) 		0.0151
(1.00) 		0.45
(1.00) 		0.513
(1.00)
5q gain 17 (4%) 457 0.13
(1.00) 		0.575
(1.00) 		0.00733
(1.00) 		0.418
(1.00) 		0.23
(1.00)
7p gain 58 (12%) 416 0.0249
(1.00) 		0.38
(1.00) 		0.079
(1.00) 		0.351
(1.00) 		0.721
(1.00)
7q gain 56 (12%) 418 0.00122
(0.383) 		0.551
(1.00) 		0.17
(1.00) 		0.155
(1.00) 		0.516
(1.00)
8p gain 105 (22%) 369 0.0747
(1.00) 		0.0266
(1.00) 		0.842
(1.00) 		0.0656
(1.00) 		0.0908
(1.00)
8q gain 135 (28%) 339 0.0125
(1.00) 		0.351
(1.00) 		0.0142
(1.00) 		0.0709
(1.00) 		0.151
(1.00)
9p gain 18 (4%) 456 0.493
(1.00) 		0.914
(1.00) 		0.18
(1.00) 		0.424
(1.00) 		0.311
(1.00)
9q gain 7 (1%) 467 0.729
(1.00) 		0.844
(1.00) 		0.189
(1.00) 		0.679
(1.00) 		0.202
(1.00)
10p gain 106 (22%) 368 0.809
(1.00) 		0.376
(1.00) 		0.864
(1.00) 		0.466
(1.00) 		0.843
(1.00)
10q gain 100 (21%) 374 0.622
(1.00) 		0.873
(1.00) 		0.926
(1.00) 		0.618
(1.00) 		0.321
(1.00)
12q gain 43 (9%) 431 0.175
(1.00) 		0.34
(1.00) 		0.129
(1.00) 		0.158
(1.00) 		0.814
(1.00)
15q gain 9 (2%) 465 0.0106
(1.00) 		0.996
(1.00) 		0.584
(1.00) 		0.456
(1.00) 		0.0754
(1.00)
16p gain 21 (4%) 453 0.625
(1.00) 		0.0678
(1.00) 		0.18
(1.00) 		0.214
(1.00) 		0.124
(1.00)
16q gain 9 (2%) 465 0.899
(1.00) 		0.086
(1.00) 		0.116
(1.00) 		0.456
(1.00) 		0.000812
(0.257)
17p gain 10 (2%) 464 0.815
(1.00) 		0.539
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.171
(1.00)
xq gain 55 (12%) 419 0.0198
(1.00) 		0.381
(1.00) 		0.688
(1.00) 		0.432
(1.00) 		0.148
(1.00)
1q loss 11 (2%) 463 0.0486
(1.00) 		0.229
(1.00) 		0.00117
(0.368) 		0.736
(1.00) 		0.00888
(1.00)
2p loss 10 (2%) 464 0.037
(1.00) 		0.0566
(1.00) 		0.626
(1.00) 		0.0692
(1.00) 		0.0998
(1.00)
2q loss 16 (3%) 458 0.00578
(1.00) 		0.0284
(1.00) 		0.42
(1.00) 		0.049
(1.00) 		0.337
(1.00)
20p loss 16 (3%) 458 0.663
(1.00) 		0.0412
(1.00) 		0.00755
(1.00) 		0.0857
(1.00) 		0.138
(1.00)
20q loss 8 (2%) 466 0.259
(1.00) 		0.434
(1.00) 		0.0083
(1.00) 		0.0455
(1.00) 		1
(1.00)
'1p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.61e-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 362 19 93
1P GAIN MUTATED 17 2 19
1P GAIN WILD-TYPE 345 17 74

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

'2p gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.21e-09 (Fisher's exact test), Q value = 3e-06

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
2P GAIN MUTATED 40 5 36
2P GAIN WILD-TYPE 322 14 57

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 = 0.0034

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
2Q GAIN MUTATED 34 4 27
2Q GAIN WILD-TYPE 328 15 66

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

'3q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.82e-08 (Fisher's exact test), Q value = 6.7e-06

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
3Q GAIN MUTATED 30 4 31
3Q GAIN WILD-TYPE 332 15 62

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

'5p gain' versus 'Time to Death'

P value = 0.000213 (logrank test), Q value = 0.07

Table S5.  Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
5P GAIN MUTATED 45 12 0.0 - 71.2 (15.0)
5P GAIN WILD-TYPE 427 47 0.1 - 191.8 (22.5)

Figure S5.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.11e-09 (Fisher's exact test), Q value = 4.1e-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 362 19 93
5P GAIN MUTATED 16 3 26
5P GAIN WILD-TYPE 346 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 = 5.58e-07 (Fisher's exact test), Q value = 2e-04

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
6P GAIN MUTATED 34 1 30
6P GAIN WILD-TYPE 328 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 = 0.000129 (Fisher's exact test), Q value = 0.043

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
6Q GAIN MUTATED 30 1 23
6Q GAIN WILD-TYPE 332 18 70

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

'11p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000312 (Fisher's exact test), Q value = 0.1

Table S9.  Gene #21: '11p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
11P GAIN MUTATED 7 0 11
11P GAIN WILD-TYPE 355 19 82

Figure S9.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q gain' versus 'Time to Death'

P value = 0.000437 (logrank test), Q value = 0.14

Table S10.  Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
11Q GAIN MUTATED 16 6 1.1 - 67.2 (16.7)
11Q GAIN WILD-TYPE 456 53 0.0 - 191.8 (22.1)

Figure S10.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'12p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000154 (Fisher's exact test), Q value = 0.051

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
12P GAIN MUTATED 30 2 23
12P GAIN WILD-TYPE 332 17 70

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

'13q gain' versus 'AGE'

P value = 0.000466 (t-test), Q value = 0.15

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
13Q GAIN MUTATED 25 69.0 (6.5)
13Q GAIN WILD-TYPE 448 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 = 1.35e-06 (Fisher's exact test), Q value = 0.00048

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
13Q GAIN MUTATED 8 1 16
13Q GAIN WILD-TYPE 354 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 = 3.11e-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 362 19 93
14Q GAIN MUTATED 14 2 19
14Q GAIN WILD-TYPE 348 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 = 0.000431 (Fisher's exact test), Q value = 0.14

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
17Q GAIN MUTATED 11 0 13
17Q GAIN WILD-TYPE 351 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 = 2.14e-15 (Fisher's exact test), Q value = 8.3e-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 362 19 93
18P GAIN MUTATED 18 4 36
18P GAIN WILD-TYPE 344 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 = 9.71e-07 (Fisher's exact test), Q value = 0.00035

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
18Q GAIN MUTATED 14 3 19
18Q GAIN WILD-TYPE 348 16 74

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

'19p gain' versus 'AGE'

P value = 3.22e-07 (t-test), Q value = 0.00012

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
19P GAIN MUTATED 43 71.2 (8.6)
19P GAIN WILD-TYPE 430 63.0 (11.2)

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

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 5.04e-07 (Fisher's exact test), Q value = 0.00018

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
19P GAIN MUTATED 18 3 22
19P GAIN WILD-TYPE 344 16 71

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

'19q gain' versus 'AGE'

P value = 2.03e-08 (t-test), Q value = 7.4e-06

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
19Q GAIN MUTATED 46 71.8 (8.7)
19Q GAIN WILD-TYPE 427 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 = 1.71e-14 (Fisher's exact test), Q value = 6.6e-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 362 19 93
19Q GAIN MUTATED 12 3 31
19Q GAIN WILD-TYPE 350 16 62

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

'20p gain' versus 'AGE'

P value = 6.52e-05 (t-test), Q value = 0.022

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
20P GAIN MUTATED 92 67.8 (10.3)
20P GAIN WILD-TYPE 381 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 = 8.24e-14 (Fisher's exact test), Q value = 3.2e-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 362 19 93
20P GAIN MUTATED 42 4 46
20P GAIN WILD-TYPE 320 15 47

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

'20q gain' versus 'Time to Death'

P value = 5e-04 (logrank test), Q value = 0.16

Table S24.  Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
20Q GAIN MUTATED 107 22 0.0 - 191.8 (15.4)
20Q GAIN WILD-TYPE 365 37 0.1 - 185.8 (23.3)

Figure S24.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'AGE'

P value = 7.26e-06 (t-test), Q value = 0.0025

Table S25.  Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
20Q GAIN MUTATED 108 67.8 (10.1)
20Q GAIN WILD-TYPE 365 62.6 (11.3)

Figure S25.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.91e-19 (Fisher's exact test), Q value = 2.7e-16

Table S26.  Gene #37: '20q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
20Q GAIN MUTATED 48 4 56
20Q GAIN WILD-TYPE 314 15 37

Figure S26.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.57e-07 (Fisher's exact test), Q value = 0.00031

Table S27.  Gene #38: '21q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
21Q GAIN MUTATED 11 0 18
21Q GAIN WILD-TYPE 351 19 75

Figure S27.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q gain' versus 'AGE'

P value = 0.000581 (t-test), Q value = 0.19

Table S28.  Gene #39: '22q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
22Q GAIN MUTATED 28 69.7 (8.4)
22Q GAIN WILD-TYPE 445 63.4 (11.3)

Figure S28.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'AGE'

'22q gain' versus 'HISTOLOGICAL.TYPE'

P value = 4.42e-10 (Fisher's exact test), Q value = 1.7e-07

Table S29.  Gene #39: '22q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
22Q GAIN MUTATED 7 1 21
22Q GAIN WILD-TYPE 355 18 72

Figure S29.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'1p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.11e-05 (Fisher's exact test), Q value = 0.017

Table S30.  Gene #41: '1p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
1P LOSS MUTATED 6 2 11
1P LOSS WILD-TYPE 356 17 82

Figure S30.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.34e-09 (Fisher's exact test), Q value = 5e-07

Table S31.  Gene #45: '3p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
3P LOSS MUTATED 16 6 23
3P LOSS WILD-TYPE 346 13 70

Figure S31.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.85e-06 (Fisher's exact test), Q value = 0.00065

Table S32.  Gene #46: '3q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
3Q LOSS MUTATED 10 1 17
3Q LOSS WILD-TYPE 352 18 76

Figure S32.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4p loss' versus 'AGE'

P value = 5.82e-05 (t-test), Q value = 0.02

Table S33.  Gene #47: '4p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
4P LOSS MUTATED 82 68.0 (9.9)
4P LOSS WILD-TYPE 391 62.9 (11.3)

Figure S33.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'AGE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.26e-20 (Fisher's exact test), Q value = 1.7e-17

Table S34.  Gene #47: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
4P LOSS MUTATED 29 4 49
4P LOSS WILD-TYPE 333 15 44

Figure S34.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'AGE'

P value = 7.32e-05 (t-test), Q value = 0.025

Table S35.  Gene #48: '4q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
4Q LOSS MUTATED 82 68.0 (10.0)
4Q LOSS WILD-TYPE 391 62.9 (11.3)

Figure S35.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #2: 'AGE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.23e-19 (Fisher's exact test), Q value = 8.8e-17

Table S36.  Gene #48: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
4Q LOSS MUTATED 29 5 48
4Q LOSS WILD-TYPE 333 14 45

Figure S36.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.51e-11 (Fisher's exact test), Q value = 9.5e-09

Table S37.  Gene #49: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
5P LOSS MUTATED 16 1 29
5P LOSS WILD-TYPE 346 18 64

Figure S37.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.21e-17 (Fisher's exact test), Q value = 8.6e-15

Table S38.  Gene #50: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
5Q LOSS MUTATED 19 3 40
5Q LOSS WILD-TYPE 343 16 53

Figure S38.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.58e-06 (Fisher's exact test), Q value = 0.0019

Table S39.  Gene #51: '6p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
6P LOSS MUTATED 3 1 11
6P LOSS WILD-TYPE 359 18 82

Figure S39.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'6q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.65e-08 (Fisher's exact test), Q value = 6.1e-06

Table S40.  Gene #52: '6q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
6Q LOSS MUTATED 4 1 16
6Q LOSS WILD-TYPE 358 18 77

Figure S40.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7p loss' versus 'AGE'

P value = 8.28e-05 (t-test), Q value = 0.028

Table S41.  Gene #53: '7p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
7P LOSS MUTATED 38 70.4 (9.8)
7P LOSS WILD-TYPE 435 63.2 (11.2)

Figure S41.  Get High-res Image Gene #53: '7p loss' versus Clinical Feature #2: 'AGE'

'7p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.85e-08 (Fisher's exact test), Q value = 2.1e-05

Table S42.  Gene #53: '7p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
7P LOSS MUTATED 14 2 22
7P LOSS WILD-TYPE 348 17 71

Figure S42.  Get High-res Image Gene #53: '7p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss' versus 'AGE'

P value = 1.45e-05 (t-test), Q value = 0.005

Table S43.  Gene #54: '7q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
7Q LOSS MUTATED 36 69.5 (7.1)
7Q LOSS WILD-TYPE 437 63.3 (11.4)

Figure S43.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #2: 'AGE'

'7q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.39e-13 (Fisher's exact test), Q value = 2.1e-10

Table S44.  Gene #54: '7q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
7Q LOSS MUTATED 8 2 26
7Q LOSS WILD-TYPE 354 17 67

Figure S44.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss' versus 'AGE'

P value = 1.33e-05 (t-test), Q value = 0.0046

Table S45.  Gene #55: '8p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
8P LOSS MUTATED 67 68.5 (8.8)
8P LOSS WILD-TYPE 406 63.0 (11.4)

Figure S45.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #2: 'AGE'

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-25 (Fisher's exact test), Q value = 4.1e-23

Table S46.  Gene #55: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
8P LOSS MUTATED 15 4 48
8P LOSS WILD-TYPE 347 15 45

Figure S46.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.26e-10 (Fisher's exact test), Q value = 4.8e-08

Table S47.  Gene #56: '8q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
8Q LOSS MUTATED 2 1 17
8Q LOSS WILD-TYPE 360 18 76

Figure S47.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'AGE'

P value = 7.27e-06 (t-test), Q value = 0.0025

Table S48.  Gene #57: '9p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
9P LOSS MUTATED 85 68.0 (8.7)
9P LOSS WILD-TYPE 388 62.8 (11.5)

Figure S48.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'AGE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.1e-20 (Fisher's exact test), Q value = 2.8e-17

Table S49.  Gene #57: '9p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
9P LOSS MUTATED 30 7 48
9P LOSS WILD-TYPE 332 12 45

Figure S49.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss' versus 'AGE'

P value = 3.47e-10 (t-test), Q value = 1.3e-07

Table S50.  Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
9Q LOSS MUTATED 102 69.3 (8.9)
9Q LOSS WILD-TYPE 371 62.2 (11.4)

Figure S50.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

'9q loss' versus 'HISTOLOGICAL.TYPE'

P value = 9.68e-19 (Fisher's exact test), Q value = 3.8e-16

Table S51.  Gene #58: '9q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
9Q LOSS MUTATED 42 8 52
9Q LOSS WILD-TYPE 320 11 41

Figure S51.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.42e-09 (Fisher's exact test), Q value = 1.6e-06

Table S52.  Gene #59: '10p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
10P LOSS MUTATED 9 3 20
10P LOSS WILD-TYPE 353 16 73

Figure S52.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00044

Table S53.  Gene #60: '10q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
10Q LOSS MUTATED 11 3 17
10Q LOSS WILD-TYPE 351 16 76

Figure S53.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p loss' versus 'AGE'

P value = 0.000312 (t-test), Q value = 0.1

Table S54.  Gene #61: '11p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
11P LOSS MUTATED 64 68.2 (10.0)
11P LOSS WILD-TYPE 409 63.1 (11.3)

Figure S54.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #2: 'AGE'

'11p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.49e-13 (Fisher's exact test), Q value = 5.7e-11

Table S55.  Gene #61: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
11P LOSS MUTATED 23 6 35
11P LOSS WILD-TYPE 339 13 58

Figure S55.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.07e-14 (Fisher's exact test), Q value = 2e-11

Table S56.  Gene #62: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
11Q LOSS MUTATED 20 7 33
11Q LOSS WILD-TYPE 342 12 60

Figure S56.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p loss' versus 'Time to Death'

P value = 0.00062 (logrank test), Q value = 0.2

Table S57.  Gene #63: '12p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
12P LOSS MUTATED 36 11 0.1 - 102.3 (21.0)
12P LOSS WILD-TYPE 436 48 0.0 - 191.8 (21.5)

Figure S57.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #1: 'Time to Death'

'12p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.01e-08 (Fisher's exact test), Q value = 1.5e-05

Table S58.  Gene #63: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
12P LOSS MUTATED 13 1 22
12P LOSS WILD-TYPE 349 18 71

Figure S58.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12q loss' versus 'Time to Death'

P value = 0.000151 (logrank test), Q value = 0.05

Table S59.  Gene #64: '12q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
12Q LOSS MUTATED 28 9 0.8 - 97.7 (18.5)
12Q LOSS WILD-TYPE 444 50 0.0 - 191.8 (22.1)

Figure S59.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #1: 'Time to Death'

'12q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.26e-08 (Fisher's exact test), Q value = 8.2e-06

Table S60.  Gene #64: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
12Q LOSS MUTATED 8 1 19
12Q LOSS WILD-TYPE 354 18 74

Figure S60.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.44e-06 (Fisher's exact test), Q value = 0.0026

Table S61.  Gene #65: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
13Q LOSS MUTATED 40 4 30
13Q LOSS WILD-TYPE 322 15 63

Figure S61.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.47e-10 (Fisher's exact test), Q value = 2.8e-07

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
14Q LOSS MUTATED 19 3 28
14Q LOSS WILD-TYPE 343 16 65

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

'15q loss' versus 'AGE'

P value = 3.03e-06 (t-test), Q value = 0.0011

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
15Q LOSS MUTATED 91 68.6 (10.5)
15Q LOSS WILD-TYPE 382 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 = 7.41e-21 (Fisher's exact test), Q value = 2.9e-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 362 19 93
15Q LOSS MUTATED 33 7 51
15Q LOSS WILD-TYPE 329 12 42

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

'16p loss' versus 'AGE'

P value = 4.29e-05 (t-test), Q value = 0.015

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
16P LOSS MUTATED 81 68.1 (10.0)
16P LOSS WILD-TYPE 392 62.8 (11.3)

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

'16p loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.85e-19 (Fisher's exact test), Q value = 3.5e-16

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
16P LOSS MUTATED 29 5 47
16P LOSS WILD-TYPE 333 14 46

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

'16q loss' versus 'AGE'

P value = 8.12e-07 (t-test), Q value = 0.00029

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
16Q LOSS MUTATED 117 67.9 (9.7)
16Q LOSS WILD-TYPE 356 62.4 (11.4)

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

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.38e-23 (Fisher's exact test), Q value = 1.3e-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 362 19 93
16Q LOSS MUTATED 49 6 62
16Q LOSS WILD-TYPE 313 13 31

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

'17p loss' versus 'AGE'

P value = 1.14e-06 (t-test), Q value = 4e-04

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
17P LOSS MUTATED 107 67.9 (9.2)
17P LOSS WILD-TYPE 366 62.5 (11.5)

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

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.91e-25 (Fisher's exact test), Q value = 7.6e-23

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
17P LOSS MUTATED 39 9 59
17P LOSS WILD-TYPE 323 10 34

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

'17q loss' versus 'AGE'

P value = 0.000154 (t-test), Q value = 0.051

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
17Q LOSS MUTATED 77 67.9 (10.0)
17Q LOSS WILD-TYPE 396 62.9 (11.3)

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

'17q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.06e-12 (Fisher's exact test), Q value = 4e-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 362 19 93
17Q LOSS MUTATED 32 7 38
17Q LOSS WILD-TYPE 330 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 = 1.45e-05 (Fisher's exact test), Q value = 0.005

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
18P LOSS MUTATED 20 5 18
18P LOSS WILD-TYPE 342 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 = 2.3e-08 (Fisher's exact test), Q value = 8.4e-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 362 19 93
18Q LOSS MUTATED 23 6 25
18Q LOSS WILD-TYPE 339 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 = 0.000199 (logrank test), Q value = 0.065

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

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
19P LOSS MUTATED 52 14 0.0 - 96.7 (15.6)
19P LOSS WILD-TYPE 420 45 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 = 2.53e-14 (Fisher's exact test), Q value = 9.7e-12

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
19P LOSS MUTATED 16 4 33
19P LOSS WILD-TYPE 346 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 = 0.000155 (logrank test), Q value = 0.051

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

nPatients nDeath Duration Range (Median), Month
ALL 472 59 0.0 - 191.8 (21.5)
19Q LOSS MUTATED 49 14 0.0 - 125.4 (14.4)
19Q LOSS WILD-TYPE 423 45 0.1 - 191.8 (22.3)

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

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.32e-12 (Fisher's exact test), Q value = 8.8e-10

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
19Q LOSS MUTATED 16 4 30
19Q LOSS WILD-TYPE 346 15 63

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

'21q loss' versus 'HISTOLOGICAL.TYPE'

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

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 362 19 93
21Q LOSS MUTATED 17 4 26
21Q LOSS WILD-TYPE 345 15 67

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

'22q loss' versus 'AGE'

P value = 9.82e-06 (t-test), Q value = 0.0034

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
22Q LOSS MUTATED 91 67.9 (9.0)
22Q LOSS WILD-TYPE 382 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 = 2.02e-14 (Fisher's exact test), Q value = 7.8e-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 362 19 93
22Q LOSS MUTATED 39 9 43
22Q LOSS WILD-TYPE 323 10 50

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

'xq loss' versus 'AGE'

P value = 0.00036 (t-test), Q value = 0.12

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

nPatients Mean (Std.Dev)
ALL 473 63.8 (11.3)
XQ LOSS MUTATED 62 68.2 (9.9)
XQ LOSS WILD-TYPE 411 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 = 1.48e-09 (Fisher's exact test), Q value = 5.5e-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 362 19 93
XQ LOSS MUTATED 27 3 32
XQ LOSS WILD-TYPE 335 16 61

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 = 474

  • 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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