Correlation between gene mutation status and selected clinical features
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1JW8DCX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1JW8DCX
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.

Summary

Testing the association between mutation status of 197 genes and 4 clinical features across 248 patients, 10 significant findings detected with Q value < 0.25.

  • PTEN mutation correlated to 'HISTOLOGICAL_TYPE'.

  • PIK3R1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • TP53 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • CTCF mutation correlated to 'HISTOLOGICAL_TYPE'.

  • FBXW7 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • ARID1A mutation correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • KRAS mutation correlated to 'HISTOLOGICAL_TYPE'.

  • CTNNB1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • PPP2R1A mutation correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 197 genes and 4 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 10 significant findings detected.

Clinical
Features 		Time
to
Death 		RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR
nMutated (%) nWild-Type logrank test Fisher's exact test Fisher's exact test Fisher's exact test
ARID1A 83 (33%) 165 0.00164
(0.143) 		0.332
(0.857) 		7e-05
(0.011) 		0.254
(0.857)
PTEN 161 (65%) 87 0.0174
(0.76) 		0.0995
(0.857) 		1e-05
(0.00197) 		0.0477
(0.857)
PIK3R1 82 (33%) 166 0.184
(0.857) 		0.405
(0.876) 		1e-05
(0.00197) 		0.951
(1.00)
TP53 69 (28%) 179 0.00425
(0.298) 		0.66
(0.921) 		1e-05
(0.00197) 		0.0475
(0.857)
CTCF 44 (18%) 204 0.14
(0.857) 		0.863
(1.00) 		0.00022
(0.0289) 		0.895
(1.00)
FBXW7 38 (15%) 210 0.79
(0.966) 		0.584
(0.906) 		0.00291
(0.229) 		0.479
(0.876)
KRAS 52 (21%) 196 0.0689
(0.857) 		0.872
(1.00) 		0.00031
(0.0349) 		0.492
(0.876)
CTNNB1 74 (30%) 174 0.656
(0.92) 		0.391
(0.876) 		1e-05
(0.00197) 		0.529
(0.906)
PPP2R1A 28 (11%) 220 0.733
(0.949) 		0.68
(0.935) 		0.00086
(0.0847) 		1
(1.00)
PIK3CA 131 (53%) 117 0.0122
(0.602) 		1
(1.00) 		0.283
(0.857) 		0.151
(0.857)
ARHGAP35 36 (15%) 212 0.922
(1.00) 		0.459
(0.876) 		0.726
(0.949) 		0.925
(1.00)
ZFHX3 44 (18%) 204 0.57
(0.906) 		0.086
(0.857) 		0.0661
(0.857) 		0.435
(0.876)
SPOP 21 (8%) 227 0.256
(0.857) 		1
(1.00) 		0.842
(0.998) 		0.569
(0.906)
FGFR2 31 (12%) 217 0.291
(0.857) 		0.843
(0.998) 		0.78
(0.958) 		0.361
(0.858)
TCP11L2 14 (6%) 234 0.0673
(0.857) 		0.582
(0.906) 		0.17
(0.857) 		0.227
(0.857)
VPS11 11 (4%) 237 0.514
(0.904) 		0.538
(0.906) 		1
(1.00) 		1
(1.00)
MAX 9 (4%) 239 0.626
(0.906) 		1
(1.00) 		0.459
(0.876) 		0.351
(0.857)
SOX17 7 (3%) 241 0.389
(0.876) 		1
(1.00) 		0.425
(0.876) 		0.675
(0.932)
CCND1 14 (6%) 234 0.439
(0.876) 		0.392
(0.876) 		0.17
(0.857) 		0.255
(0.857)
NRAS 9 (4%) 239 0.169
(0.857) 		0.492
(0.876) 		1
(1.00) 		1
(1.00)
EP300 21 (8%) 227 0.272
(0.857) 		0.486
(0.876) 		0.0664
(0.857) 		1
(1.00)
KLHL8 12 (5%) 236 0.483
(0.876) 		0.763
(0.952) 		0.289
(0.857) 		0.212
(0.857)
ALG8 11 (4%) 237 0.657
(0.92) 		0.751
(0.949) 		0.352
(0.857) 		0.593
(0.906)
GNPTAB 20 (8%) 228 0.0761
(0.857) 		0.146
(0.857) 		0.268
(0.857) 		0.578
(0.906)
SIN3A 21 (8%) 227 0.214
(0.857) 		0.155
(0.857) 		0.276
(0.857) 		0.892
(1.00)
ARID5B 29 (12%) 219 0.82
(0.988) 		0.066
(0.857) 		0.0106
(0.556) 		0.0915
(0.857)
NFE2L2 14 (6%) 234 0.491
(0.876) 		0.267
(0.857) 		0.172
(0.857) 		0.848
(0.998)
ZNF471 15 (6%) 233 0.844
(0.998) 		0.268
(0.857) 		0.14
(0.857) 		0.36
(0.858)
MORC4 20 (8%) 228 0.0577
(0.857) 		0.81
(0.983) 		0.27
(0.857) 		1
(1.00)
SELP 10 (4%) 238 0.54
(0.906) 		0.333
(0.857) 		0.335
(0.857) 		0.247
(0.857)
RBMX 12 (5%) 236 0.914
(1.00) 		0.763
(0.952) 		0.291
(0.857) 		0.0788
(0.857)
FAT1 40 (16%) 208 0.0307
(0.857) 		0.86
(1.00) 		0.0456
(0.857) 		0.772
(0.958)
MARK3 11 (4%) 237 0.47
(0.876) 		0.751
(0.949) 		0.354
(0.857) 		0.197
(0.857)
SOS1 12 (5%) 236 0.178
(0.857) 		1
(1.00) 		0.289
(0.857) 		0.836
(0.998)
RBBP6 22 (9%) 226 0.206
(0.857) 		0.817
(0.986) 		0.0433
(0.857) 		0.498
(0.882)
ZNF263 7 (3%) 241 0.278
(0.857) 		1
(1.00) 		0.426
(0.876) 		0.2
(0.857)
INTS7 8 (3%) 240 0.169
(0.857) 		0.714
(0.949) 		0.437
(0.876) 		0.53
(0.906)
L1TD1 16 (6%) 232 0.115
(0.857) 		0.425
(0.876) 		0.121
(0.857) 		0.878
(1.00)
NAT1 7 (3%) 241 0.896
(1.00) 		1
(1.00) 		0.429
(0.876) 		0.467
(0.876)
JAKMIP2 12 (5%) 236 0.356
(0.857) 		0.544
(0.906) 		0.288
(0.857) 		0.259
(0.857)
ING1 12 (5%) 236 0.196
(0.857) 		0.763
(0.952) 		0.291
(0.857) 		1
(1.00)
CCDC6 6 (2%) 242 0.46
(0.876) 		1
(1.00) 		0.361
(0.858) 		1
(1.00)
ZNF781 10 (4%) 238 0.256
(0.857) 		0.0975
(0.857) 		0.334
(0.857) 		0.479
(0.876)
MKI67 29 (12%) 219 0.0786
(0.857) 		0.312
(0.857) 		0.0105
(0.556) 		0.236
(0.857)
EIF2S2 9 (4%) 239 0.222
(0.857) 		0.492
(0.876) 		0.456
(0.876) 		0.339
(0.857)
BCOR 30 (12%) 218 0.0712
(0.857) 		0.545
(0.906) 		0.00814
(0.493) 		0.362
(0.858)
RASA1 21 (8%) 227 0.0429
(0.857) 		0.242
(0.857) 		0.567
(0.906) 		1
(1.00)
DNER 18 (7%) 230 0.299
(0.857) 		0.806
(0.98) 		0.416
(0.876) 		0.629
(0.906)
C9ORF23 9 (4%) 239 0.295
(0.857) 		1
(1.00) 		0.457
(0.876) 		1
(1.00)
CUX1 21 (8%) 227 0.208
(0.857) 		0.817
(0.986) 		0.275
(0.857) 		0.806
(0.98)
CDK17 14 (6%) 234 0.402
(0.876) 		0.267
(0.857) 		0.126
(0.857) 		0.268
(0.857)
USP28 10 (4%) 238 0.127
(0.857) 		0.333
(0.857) 		0.333
(0.857) 		0.778
(0.958)
MSH6 17 (7%) 231 0.223
(0.857) 		1
(1.00) 		0.491
(0.876) 		0.6
(0.906)
WDR45 11 (4%) 237 0.665
(0.924) 		1
(1.00) 		0.355
(0.857) 		0.527
(0.906)
C14ORF166B 9 (4%) 239 0.205
(0.857) 		0.0284
(0.857) 		0.455
(0.876) 		1
(1.00)
ATM 29 (12%) 219 0.0161
(0.745) 		0.312
(0.857) 		0.0745
(0.857) 		0.903
(1.00)
RAE1 11 (4%) 237 0.172
(0.857) 		0.0595
(0.857) 		0.743
(0.949) 		1
(1.00)
ZNF485 9 (4%) 239 0.84
(0.998) 		0.161
(0.857) 		0.456
(0.876) 		0.0691
(0.857)
POLE 27 (11%) 221 0.276
(0.857) 		0.291
(0.857) 		0.127
(0.857) 		0.399
(0.876)
AHCYL1 6 (2%) 242 0.295
(0.857) 		1
(1.00) 		0.632
(0.906) 		0.396
(0.876)
ZNF334 17 (7%) 231 0.467
(0.876) 		0.609
(0.906) 		0.807
(0.98) 		0.599
(0.906)
SACS 26 (10%) 222 0.0915
(0.857) 		0.668
(0.926) 		0.122
(0.857) 		0.626
(0.906)
MSH4 15 (6%) 233 0.0891
(0.857) 		0.582
(0.906) 		0.142
(0.857) 		0.628
(0.906)
SLC26A8 12 (5%) 236 0.184
(0.857) 		0.544
(0.906) 		0.288
(0.857) 		0.689
(0.937)
KIF20B 21 (8%) 227 0.212
(0.857) 		0.486
(0.876) 		0.0654
(0.857) 		0.904
(1.00)
RRAS2 4 (2%) 244 0.485
(0.876) 		0.626
(0.906) 		1
(1.00) 		0.43
(0.876)
CTNND1 19 (8%) 229 0.559
(0.906) 		1
(1.00) 		0.43
(0.876) 		0.377
(0.876)
NFE2L3 12 (5%) 236 0.956
(1.00) 		0.365
(0.865) 		0.218
(0.857) 		0.407
(0.876)
FAM65B 16 (6%) 232 0.0806
(0.857) 		0.791
(0.966) 		0.478
(0.876) 		0.863
(1.00)
RNF43 12 (5%) 236 0.148
(0.857) 		0.0343
(0.857) 		0.288
(0.857) 		0.638
(0.906)
MRPL47 6 (2%) 242 0.372
(0.871) 		0.419
(0.876) 		1
(1.00) 		0.467
(0.876)
TIGD4 13 (5%) 235 0.147
(0.857) 		0.773
(0.958) 		0.3
(0.857) 		0.592
(0.906)
FILIP1 16 (6%) 232 0.0656
(0.857) 		1
(1.00) 		0.473
(0.876) 		0.594
(0.906)
SLC1A3 12 (5%) 236 0.528
(0.906) 		1
(1.00) 		1
(1.00) 		0.64
(0.907)
UFSP2 11 (4%) 237 0.144
(0.857) 		1
(1.00) 		0.351
(0.857) 		0.683
(0.935)
WBP4 8 (3%) 240 0.339
(0.857) 		0.264
(0.857) 		0.438
(0.876) 		1
(1.00)
TRIM59 9 (4%) 239 0.242
(0.857) 		0.492
(0.876) 		0.454
(0.876) 		1
(1.00)
RSBN1L 12 (5%) 236 0.106
(0.857) 		0.544
(0.906) 		0.754
(0.949) 		0.156
(0.857)
SERHL2 6 (2%) 242 0.239
(0.857) 		0.196
(0.857) 		0.635
(0.906) 		1
(1.00)
OR52I2 8 (3%) 240 0.731
(0.949) 		1
(1.00) 		0.156
(0.857) 		0.78
(0.958)
SGK1 13 (5%) 235 0.519
(0.906) 		1
(1.00) 		0.572
(0.906) 		0.0486
(0.857)
LNX2 14 (6%) 234 0.119
(0.857) 		0.09
(0.857) 		0.171
(0.857) 		0.763
(0.952)
ALPK2 19 (8%) 229 0.0396
(0.857) 		0.33
(0.857) 		0.429
(0.876) 		0.24
(0.857)
REV3L 20 (8%) 228 0.0612
(0.857) 		0.336
(0.857) 		0.0691
(0.857) 		0.916
(1.00)
CAB39L 8 (3%) 240 0.228
(0.857) 		0.264
(0.857) 		0.437
(0.876) 		1
(1.00)
ERBB3 17 (7%) 231 0.121
(0.857) 		0.795
(0.97) 		0.492
(0.876) 		0.274
(0.857)
INPP4B 12 (5%) 236 0.399
(0.876) 		0.00453
(0.298) 		0.289
(0.857) 		0.167
(0.857)
C1ORF100 9 (4%) 239 0.131
(0.857) 		1
(1.00) 		0.456
(0.876) 		0.466
(0.876)
IL20 7 (3%) 241 0.232
(0.857) 		0.71
(0.949) 		0.424
(0.876) 		0.103
(0.857)
SLC44A3 6 (2%) 242 0.297
(0.857) 		1
(1.00) 		0.634
(0.906) 		0.609
(0.906)
TAP1 8 (3%) 240 0.61
(0.906) 		0.714
(0.949) 		0.434
(0.876) 		1
(1.00)
RHBDD3 4 (2%) 244 0.394
(0.876) 		0.626
(0.906) 		1
(1.00) 		1
(1.00)
BRDT 14 (6%) 234 0.121
(0.857) 		0.09
(0.857) 		0.171
(0.857) 		0.631
(0.906)
RB1 20 (8%) 228 0.179
(0.857) 		0.146
(0.857) 		0.0688
(0.857) 		0.866
(1.00)
MFAP5 9 (4%) 239 0.232
(0.857) 		1
(1.00) 		1
(1.00) 		0.529
(0.906)
NAA15 14 (6%) 234 0.304
(0.857) 		0.776
(0.958) 		0.584
(0.906) 		0.763
(0.952)
ZRANB3 7 (3%) 241 0.204
(0.857) 		0.71
(0.949) 		1
(1.00) 		1
(1.00)
SLC34A3 6 (2%) 242 0.367
(0.865) 		0.672
(0.929) 		0.63
(0.906) 		1
(1.00)
MLH3 17 (7%) 231 0.37
(0.869) 		0.609
(0.906) 		0.491
(0.876) 		0.24
(0.857)
CCDC147 15 (6%) 233 0.13
(0.857) 		0.268
(0.857) 		0.468
(0.876) 		0.589
(0.906)
ZNF662 13 (5%) 235 0.107
(0.857) 		0.773
(0.958) 		0.578
(0.906) 		0.637
(0.906)
PSMC4 11 (4%) 237 0.198
(0.857) 		1
(1.00) 		0.351
(0.857) 		0.847
(0.998)
CCDC160 11 (4%) 237 0.148
(0.857) 		0.751
(0.949) 		0.35
(0.857) 		0.832
(0.996)
PPIL4 11 (4%) 237 0.207
(0.857) 		0.538
(0.906) 		0.745
(0.949) 		0.593
(0.906)
CCDC144A 18 (7%) 230 0.314
(0.857) 		0.215
(0.857) 		0.66
(0.921) 		0.294
(0.857)
TUBGCP6 20 (8%) 228 0.426
(0.876) 		0.632
(0.906) 		0.0682
(0.857) 		0.377
(0.876)
TTC39C 7 (3%) 241 0.255
(0.857) 		0.0495
(0.857) 		0.427
(0.876) 		1
(1.00)
COL8A1 10 (4%) 238 0.67
(0.928) 		1
(1.00) 		0.335
(0.857) 		0.467
(0.876)
PER3 12 (5%) 236 0.154
(0.857) 		0.544
(0.906) 		0.288
(0.857) 		1
(1.00)
MGA 26 (10%) 222 0.966
(1.00) 		1
(1.00) 		0.35
(0.857) 		0.146
(0.857)
GPRASP1 21 (8%) 227 0.201
(0.857) 		0.817
(0.986) 		0.275
(0.857) 		0.585
(0.906)
PPM1D 11 (4%) 237 0.156
(0.857) 		0.0595
(0.857) 		0.352
(0.857) 		0.584
(0.906)
ZNF674 14 (6%) 234 0.083
(0.857) 		0.582
(0.906) 		0.582
(0.906) 		0.518
(0.906)
LIMK2 12 (5%) 236 0.212
(0.857) 		0.544
(0.906) 		0.754
(0.949) 		0.685
(0.935)
ZNF606 16 (6%) 232 0.301
(0.857) 		0.18
(0.857) 		0.12
(0.857) 		0.498
(0.882)
SFRP4 8 (3%) 240 0.197
(0.857) 		0.714
(0.949) 		0.438
(0.876) 		0.336
(0.857)
TXNRD1 8 (3%) 240 0.136
(0.857) 		0.264
(0.857) 		0.436
(0.876) 		0.349
(0.857)
LETMD1 6 (2%) 242 0.195
(0.857) 		1
(1.00) 		0.632
(0.906) 		0.0524
(0.857)
ZNF721 13 (5%) 235 0.16
(0.857) 		0.384
(0.876) 		0.304
(0.857) 		0.634
(0.906)
RASSF9 9 (4%) 239 0.204
(0.857) 		0.161
(0.857) 		0.455
(0.876) 		0.59
(0.906)
AGXT2 11 (4%) 237 0.776
(0.958) 		0.751
(0.949) 		0.351
(0.857) 		0.634
(0.906)
MECOM 12 (5%) 236 0.109
(0.857) 		0.544
(0.906) 		0.288
(0.857) 		1
(1.00)
ATP6V1C2 12 (5%) 236 0.136
(0.857) 		1
(1.00) 		0.291
(0.857) 		0.835
(0.998)
DYM 10 (4%) 238 0.829
(0.994) 		0.75
(0.949) 		0.745
(0.949) 		1
(1.00)
TAB3 18 (7%) 230 0.0696
(0.857) 		0.46
(0.876) 		0.0864
(0.857) 		0.259
(0.857)
ZNF649 14 (6%) 234 0.117
(0.857) 		0.267
(0.857) 		0.172
(0.857) 		0.761
(0.952)
FN1 24 (10%) 224 0.16
(0.857) 		0.826
(0.992) 		0.0219
(0.857) 		0.373
(0.871)
CCDC150 11 (4%) 237 0.246
(0.857) 		0.751
(0.949) 		0.743
(0.949) 		0.848
(0.998)
KIF21A 15 (6%) 233 0.109
(0.857) 		0.0575
(0.857) 		0.14
(0.857) 		0.591
(0.906)
BHLHB9 8 (3%) 240 0.236
(0.857) 		1
(1.00) 		0.435
(0.876) 		0.732
(0.949)
EXOSC9 10 (4%) 238 0.72
(0.949) 		0.333
(0.857) 		0.332
(0.857) 		0.586
(0.906)
ZKSCAN1 7 (3%) 241 0.329
(0.857) 		0.71
(0.949) 		1
(1.00) 		0.736
(0.949)
OR8B8 7 (3%) 241 0.273
(0.857) 		0.428
(0.876) 		0.428
(0.876) 		0.399
(0.876)
SENP7 12 (5%) 236 0.381
(0.876) 		0.544
(0.906) 		0.29
(0.857) 		0.686
(0.935)
WDR65 6 (2%) 242 0.432
(0.876) 		0.419
(0.876) 		0.634
(0.906) 		1
(1.00)
NRIP1 13 (5%) 235 0.417
(0.876) 		0.384
(0.876) 		0.574
(0.906) 		0.407
(0.876)
MCTP1 13 (5%) 235 0.134
(0.857) 		1
(1.00) 		0.576
(0.906) 		0.636
(0.906)
CCDC146 14 (6%) 234 0.125
(0.857) 		0.09
(0.857) 		0.172
(0.857) 		0.635
(0.906)
ZNF620 9 (4%) 239 0.239
(0.857) 		0.492
(0.876) 		0.458
(0.876) 		0.733
(0.949)
PTPN12 10 (4%) 238 0.656
(0.92) 		0.333
(0.857) 		0.335
(0.857) 		0.586
(0.906)
RIOK3 9 (4%) 239 0.239
(0.857) 		0.161
(0.857) 		0.455
(0.876) 		1
(1.00)
CASP8 17 (7%) 231 0.787
(0.964) 		0.609
(0.906) 		0.491
(0.876) 		0.526
(0.906)
GFAP 6 (2%) 242 0.341
(0.857) 		1
(1.00) 		0.635
(0.906) 		0.324
(0.857)
OMA1 10 (4%) 238 0.233
(0.857) 		0.0975
(0.857) 		0.333
(0.857) 		0.527
(0.906)
DENND3 15 (6%) 233 0.313
(0.857) 		0.419
(0.876) 		0.474
(0.876) 		0.88
(1.00)
CHEK2 12 (5%) 236 0.556
(0.906) 		0.22
(0.857) 		0.754
(0.949) 		0.134
(0.857)
ZMYM2 17 (7%) 231 0.262
(0.857) 		0.304
(0.857) 		0.0992
(0.857) 		0.662
(0.921)
EPC2 5 (2%) 243 0.295
(0.857) 		0.655
(0.92) 		0.622
(0.906) 		1
(1.00)
DEPDC1B 11 (4%) 237 0.778
(0.958) 		1
(1.00) 		0.744
(0.949) 		0.157
(0.857)
C3AR1 7 (3%) 241 0.125
(0.857) 		1
(1.00) 		0.428
(0.876) 		0.53
(0.906)
STK3 10 (4%) 238 0.196
(0.857) 		0.505
(0.89) 		0.338
(0.857) 		1
(1.00)
FOXJ3 10 (4%) 238 0.184
(0.857) 		0.75
(0.949) 		0.335
(0.857) 		0.637
(0.906)
EPS8 12 (5%) 236 0.651
(0.92) 		1
(1.00) 		0.754
(0.949) 		0.684
(0.935)
ZNF385B 7 (3%) 241 0.332
(0.857) 		0.428
(0.876) 		0.427
(0.876) 		1
(1.00)
EFCAB4B 11 (4%) 237 0.132
(0.857) 		0.751
(0.949) 		0.353
(0.857) 		0.336
(0.857)
NPRL2 5 (2%) 243 0.963
(1.00) 		0.655
(0.92) 		0.622
(0.906) 		0.247
(0.857)
ATF6 14 (6%) 234 0.0996
(0.857) 		1
(1.00) 		0.583
(0.906) 		0.632
(0.906)
LIMA1 8 (3%) 240 0.203
(0.857) 		0.714
(0.949) 		0.439
(0.876) 		1
(1.00)
PPIG 16 (6%) 232 0.142
(0.857) 		0.596
(0.906) 		0.119
(0.857) 		0.904
(1.00)
ZNF774 10 (4%) 238 0.194
(0.857) 		0.75
(0.949) 		0.741
(0.949) 		0.586
(0.906)
MUTED 7 (3%) 241 0.273
(0.857) 		0.428
(0.876) 		0.426
(0.876) 		1
(1.00)
TPX2 6 (2%) 242 0.346
(0.857) 		1
(1.00) 		0.634
(0.906) 		0.132
(0.857)
PARG 9 (4%) 239 0.226
(0.857) 		1
(1.00) 		0.454
(0.876) 		1
(1.00)
PSMD3 11 (4%) 237 0.147
(0.857) 		1
(1.00) 		0.745
(0.949) 		1
(1.00)
STRN3 12 (5%) 236 0.168
(0.857) 		0.544
(0.906) 		0.753
(0.949) 		0.595
(0.906)
MLL4 30 (12%) 218 0.0227
(0.857) 		0.84
(0.998) 		0.0434
(0.857) 		0.572
(0.906)
MSN 15 (6%) 233 0.291
(0.857) 		1
(1.00) 		0.598
(0.906) 		0.483
(0.876)
MAPK8 11 (4%) 237 0.147
(0.857) 		0.337
(0.857) 		0.352
(0.857) 		0.309
(0.857)
RBL2 12 (5%) 236 0.458
(0.876) 		1
(1.00) 		0.289
(0.857) 		0.159
(0.857)
PDGFRA 12 (5%) 236 0.412
(0.876) 		0.544
(0.906) 		0.287
(0.857) 		1
(1.00)
TMEM62 9 (4%) 239 0.222
(0.857) 		0.492
(0.876) 		0.457
(0.876) 		0.586
(0.906)
RG9MTD3 8 (3%) 240 0.699
(0.948) 		0.264
(0.857) 		0.681
(0.935) 		0.35
(0.857)
KANK4 11 (4%) 237 0.84
(0.998) 		0.751
(0.949) 		0.747
(0.949) 		1
(1.00)
MYOM1 23 (9%) 225 0.779
(0.958) 		0.823
(0.99) 		0.848
(0.998) 		0.439
(0.876)
MORC3 10 (4%) 238 0.176
(0.857) 		1
(1.00) 		0.739
(0.949) 		0.4
(0.876)
CCDC82 12 (5%) 236 0.473
(0.876) 		0.544
(0.906) 		0.29
(0.857) 		0.593
(0.906)
B3GALT5 4 (2%) 244 0.504
(0.89) 		0.3
(0.857) 		1
(1.00) 		1
(1.00)
NOC3L 11 (4%) 237 0.155
(0.857) 		0.337
(0.857) 		0.353
(0.857) 		0.638
(0.906)
NSUN4 6 (2%) 242 0.317
(0.857) 		0.419
(0.876) 		1
(1.00) 		0.609
(0.906)
ASXL2 14 (6%) 234 0.103
(0.857) 		0.582
(0.906) 		0.584
(0.906) 		0.204
(0.857)
CHD4 35 (14%) 213 0.695
(0.944) 		0.346
(0.857) 		0.454
(0.876) 		1
(1.00)
FCN1 7 (3%) 241 0.946
(1.00) 		1
(1.00) 		0.427
(0.876) 		1
(1.00)
NIPA2 8 (3%) 240 0.28
(0.857) 		0.714
(0.949) 		1
(1.00) 		1
(1.00)
C14ORF118 13 (5%) 235 0.172
(0.857) 		0.141
(0.857) 		0.302
(0.857) 		0.726
(0.949)
THAP5 6 (2%) 242 0.326
(0.857) 		0.0883
(0.857) 		0.634
(0.906) 		1
(1.00)
ZNF611 12 (5%) 236 0.637
(0.906) 		1
(1.00) 		0.287
(0.857) 		0.166
(0.857)
ZCCHC18 6 (2%) 242 0.348
(0.857) 		0.0883
(0.857) 		0.634
(0.906) 		1
(1.00)
PRKCE 9 (4%) 239 0.196
(0.857) 		0.728
(0.949) 		0.456
(0.876) 		1
(1.00)
BMP2K 13 (5%) 235 0.161
(0.857) 		0.384
(0.876) 		0.303
(0.857) 		0.685
(0.935)
PRPF38B 11 (4%) 237 0.211
(0.857) 		0.751
(0.949) 		0.351
(0.857) 		0.635
(0.906)
LGMN 7 (3%) 241 0.361
(0.858) 		0.71
(0.949) 		0.428
(0.876) 		0.28
(0.857)
SSH2 12 (5%) 236 0.176
(0.857) 		0.544
(0.906) 		0.754
(0.949) 		0.593
(0.906)
EMR1 11 (4%) 237 0.18
(0.857) 		0.337
(0.857) 		0.352
(0.857) 		0.587
(0.906)
OR5AK2 5 (2%) 243 0.238
(0.857) 		0.655
(0.92) 		0.622
(0.906) 		0.322
(0.857)
C1ORF101 12 (5%) 236 0.168
(0.857) 		0.544
(0.906) 		0.287
(0.857) 		0.725
(0.949)
ZNF534 9 (4%) 239 0.249
(0.857) 		0.492
(0.876) 		0.456
(0.876) 		0.586
(0.906)
FAM122A 6 (2%) 242 0.992
(1.00) 		1
(1.00) 		0.634
(0.906) 		0.282
(0.857)
'PTEN MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

Table S1.  Gene #1: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
PTEN MUTATED 159 1 1
PTEN WILD-TYPE 41 3 43

Figure S1.  Get High-res Image Gene #1: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'PIK3R1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

Table S2.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
PIK3R1 MUTATED 79 1 2
PIK3R1 WILD-TYPE 121 3 42

Figure S2.  Get High-res Image Gene #2: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

Table S3.  Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
TP53 MUTATED 27 3 39
TP53 WILD-TYPE 173 1 5

Figure S3.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'CTCF MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.029

Table S4.  Gene #4: 'CTCF MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
CTCF MUTATED 44 0 0
CTCF WILD-TYPE 156 4 44

Figure S4.  Get High-res Image Gene #4: 'CTCF MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'FBXW7 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00291 (Fisher's exact test), Q value = 0.23

Table S5.  Gene #5: 'FBXW7 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
FBXW7 MUTATED 23 1 14
FBXW7 WILD-TYPE 177 3 30

Figure S5.  Get High-res Image Gene #5: 'FBXW7 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'ARID1A MUTATION STATUS' versus 'Time to Death'

P value = 0.00164 (logrank test), Q value = 0.14

Table S6.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 248 33 0.6 - 185.8 (35.9)
ARID1A MUTATED 83 3 1.0 - 129.8 (37.5)
ARID1A WILD-TYPE 165 30 0.6 - 185.8 (34.6)

Figure S6.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ARID1A MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.011

Table S7.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
ARID1A MUTATED 78 1 4
ARID1A WILD-TYPE 122 3 40

Figure S7.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'KRAS MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00031 (Fisher's exact test), Q value = 0.035

Table S8.  Gene #9: 'KRAS MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
KRAS MUTATED 51 0 1
KRAS WILD-TYPE 149 4 43

Figure S8.  Get High-res Image Gene #9: 'KRAS MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'CTNNB1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

Table S9.  Gene #10: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
CTNNB1 MUTATED 74 0 0
CTNNB1 WILD-TYPE 126 4 44

Figure S9.  Get High-res Image Gene #10: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

'PPP2R1A MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00086 (Fisher's exact test), Q value = 0.085

Table S10.  Gene #16: 'PPP2R1A MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 200 4 44
PPP2R1A MUTATED 15 1 12
PPP2R1A WILD-TYPE 185 3 32

Figure S10.  Get High-res Image Gene #16: 'PPP2R1A MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL_TYPE'

Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/22815333/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/22507145/UCEC-TP.merged_data.txt

  • Number of patients = 248

  • Number of significantly mutated genes = 197

  • Number of selected clinical features = 4

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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