Uterine Corpus Endometrioid Carcinoma: Correlation between gene mutation status and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between mutation status of 123 genes and 5 clinical features across 248 patients, 9 significant findings detected with Q value < 0.25.

  • PTEN mutation correlated to 'HISTOLOGICAL.TYPE'.

  • CTNNB1 mutation correlated to 'HISTOLOGICAL.TYPE'.

  • KRAS mutation correlated to 'AGE'.

  • TP53 mutation correlated to 'AGE',  'HISTOLOGICAL.TYPE', and 'NEOADJUVANT.THERAPY'.

  • SAP30 mutation correlated to 'HISTOLOGICAL.TYPE'.

  • ZNF69 mutation correlated to 'HISTOLOGICAL.TYPE'.

  • ANKRD31 mutation correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 123 genes and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NEOADJUVANT
THERAPY
nMutated (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test
TP53 69 (28%) 179 0.325
(1.00) 		6.15e-06
(0.00376) 		3.98e-23
(2.45e-20) 		0.371
(1.00) 		6.08e-05
(0.037)
PTEN 161 (65%) 87 0.19
(1.00) 		0.0276
(1.00) 		5.44e-19
(3.34e-16) 		0.0503
(1.00) 		0.0016
(0.956)
CTNNB1 74 (30%) 174 0.878
(1.00) 		0.0017
(1.00) 		1.04e-05
(0.00636) 		0.381
(1.00) 		0.0124
(1.00)
KRAS 53 (21%) 195 0.072
(1.00) 		0.000274
(0.166) 		0.00692
(1.00) 		0.253
(1.00) 		0.00892
(1.00)
SAP30 4 (2%) 244 0.648
(1.00) 		0.57
(1.00) 		1.34e-08
(8.19e-06) 		1
(1.00) 		0.577
(1.00)
ZNF69 7 (3%) 241 0.514
(1.00) 		0.0163
(1.00) 		0.000147
(0.0892) 		1
(1.00) 		0.396
(1.00)
ANKRD31 17 (7%) 231 0.2
(1.00) 		0.964
(1.00) 		4.87e-05
(0.0297) 		0.432
(1.00) 		1
(1.00)
FBXW7 39 (16%) 209 0.772
(1.00) 		0.904
(1.00) 		0.0473
(1.00) 		0.855
(1.00) 		0.117
(1.00)
SPOP 21 (8%) 227 0.65
(1.00) 		0.527
(1.00) 		0.332
(1.00) 		0.811
(1.00) 		0.452
(1.00)
CTCF 45 (18%) 203 0.405
(1.00) 		0.0198
(1.00) 		0.0021
(1.00) 		0.863
(1.00) 		1
(1.00)
PIK3CA 132 (53%) 116 0.055
(1.00) 		0.195
(1.00) 		0.555
(1.00) 		0.593
(1.00) 		0.887
(1.00)
PIK3R1 83 (33%) 165 0.871
(1.00) 		0.806
(1.00) 		0.000827
(0.499) 		0.395
(1.00) 		0.293
(1.00)
PPP2R1A 27 (11%) 221 0.121
(1.00) 		0.0374
(1.00) 		0.00977
(1.00) 		0.52
(1.00) 		0.112
(1.00)
PRKAR1B 4 (2%) 244 0.702
(1.00) 		0.978
(1.00) 		0.961
(1.00) 		0.608
(1.00) 		1
(1.00)
FGFR2 31 (12%) 217 0.9
(1.00) 		0.998
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.39
(1.00)
ARID1A 83 (33%) 165 0.008
(1.00) 		0.00721
(1.00) 		0.00127
(0.759) 		0.673
(1.00) 		0.0234
(1.00)
CHD4 35 (14%) 213 0.361
(1.00) 		0.418
(1.00) 		0.779
(1.00) 		0.565
(1.00) 		0.683
(1.00)
NFE2L2 15 (6%) 233 0.903
(1.00) 		0.191
(1.00) 		0.447
(1.00) 		0.589
(1.00) 		1
(1.00)
P2RY11 9 (4%) 239 0.395
(1.00) 		0.396
(1.00) 		0.987
(1.00) 		0.497
(1.00) 		0.709
(1.00)
CCND1 15 (6%) 233 0.729
(1.00) 		0.0556
(1.00) 		0.413
(1.00) 		0.4
(1.00) 		0.13
(1.00)
SOX17 7 (3%) 241 0.669
(1.00) 		0.848
(1.00) 		0.00567
(1.00) 		0.428
(1.00) 		0.677
(1.00)
FOXA2 12 (5%) 236 0.799
(1.00) 		0.531
(1.00) 		0.972
(1.00) 		0.229
(1.00) 		1
(1.00)
FAM9A 14 (6%) 234 0.378
(1.00) 		0.913
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.121
(1.00)
DNER 18 (7%) 230 0.746
(1.00) 		0.0414
(1.00) 		0.0324
(1.00) 		0.44
(1.00) 		0.277
(1.00)
SMTNL2 9 (4%) 239 0.472
(1.00) 		0.53
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.451
(1.00)
RBMX 13 (5%) 235 0.336
(1.00) 		0.161
(1.00) 		0.4
(1.00) 		0.142
(1.00) 		0.756
(1.00)
PGR 12 (5%) 236 0.268
(1.00) 		0.228
(1.00) 		0.0105
(1.00) 		1
(1.00) 		0.52
(1.00)
TNFAIP6 12 (5%) 236 0.819
(1.00) 		0.302
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.741
(1.00)
SGK1 15 (6%) 233 0.925
(1.00) 		0.427
(1.00) 		0.759
(1.00) 		0.158
(1.00) 		0.563
(1.00)
PDE8B 16 (6%) 232 0.196
(1.00) 		0.135
(1.00) 		0.0275
(1.00) 		1
(1.00) 		0.568
(1.00)
HPD 7 (3%) 241 0.43
(1.00) 		0.0538
(1.00) 		0.0585
(1.00) 		1
(1.00) 		1
(1.00)
RPL14 7 (3%) 241 0.532
(1.00) 		0.677
(1.00) 		0.991
(1.00) 		0.428
(1.00) 		0.396
(1.00)
TAP1 8 (3%) 240 0.588
(1.00) 		0.877
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.452
(1.00)
MAX 11 (4%) 237 0.889
(1.00) 		0.336
(1.00) 		0.404
(1.00) 		0.753
(1.00) 		0.732
(1.00)
ZNF286A 12 (5%) 236 0.308
(1.00) 		0.518
(1.00) 		0.00262
(1.00) 		0.229
(1.00) 		1
(1.00)
RASA1 22 (9%) 226 0.127
(1.00) 		0.466
(1.00) 		0.0211
(1.00) 		0.639
(1.00) 		0.803
(1.00)
ABI1 4 (2%) 244 0.663
(1.00) 		0.0342
(1.00) 		0.961
(1.00) 		0.302
(1.00) 		0.303
(1.00)
NRAS 9 (4%) 239 0.354
(1.00) 		0.616
(1.00) 		0.0289
(1.00) 		0.722
(1.00) 		0.451
(1.00)
ZNF367 8 (3%) 240 0.449
(1.00) 		0.365
(1.00) 		0.628
(1.00) 		0.127
(1.00) 		1
(1.00)
ING1 13 (5%) 235 0.37
(1.00) 		0.694
(1.00) 		0.178
(1.00) 		0.142
(1.00) 		1
(1.00)
MFGE8 4 (2%) 244 0.533
(1.00) 		0.127
(1.00) 		0.0702
(1.00) 		1
(1.00) 		0.303
(1.00)
ZNF267 16 (6%) 232 0.565
(1.00) 		0.207
(1.00) 		0.0275
(1.00) 		0.79
(1.00) 		1
(1.00)
ARID5B 29 (12%) 219 0.642
(1.00) 		0.649
(1.00) 		0.00865
(1.00) 		1
(1.00) 		0.508
(1.00)
DYRK1A 12 (5%) 236 0.939
(1.00) 		0.386
(1.00) 		0.595
(1.00) 		0.552
(1.00) 		1
(1.00)
EMB 8 (3%) 240 0.443
(1.00) 		0.497
(1.00) 		0.000594
(0.359) 		0.719
(1.00) 		0.452
(1.00)
ESR1 11 (4%) 237 0.329
(1.00) 		0.317
(1.00) 		0.653
(1.00) 		0.518
(1.00) 		0.179
(1.00)
NAA30 8 (3%) 240 0.565
(1.00) 		0.358
(1.00) 		0.518
(1.00) 		0.719
(1.00) 		0.688
(1.00)
CHSY3 10 (4%) 238 0.862
(1.00) 		0.00805
(1.00) 		0.62
(1.00) 		0.739
(1.00) 		0.468
(1.00)
SIN3A 21 (8%) 227 0.574
(1.00) 		0.256
(1.00) 		0.1
(1.00) 		0.811
(1.00) 		0.609
(1.00)
CYLC1 18 (7%) 230 0.198
(1.00) 		0.765
(1.00) 		0.000601
(0.363) 		0.313
(1.00) 		0.413
(1.00)
METTL14 10 (4%) 238 0.358
(1.00) 		0.833
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.293
(1.00)
MORC4 20 (8%) 228 0.152
(1.00) 		0.0204
(1.00) 		0.629
(1.00) 		1
(1.00) 		0.295
(1.00)
TAB3 18 (7%) 230 0.22
(1.00) 		0.107
(1.00) 		0.00686
(1.00) 		0.616
(1.00) 		1
(1.00)
TPTE 15 (6%) 233 0.273
(1.00) 		0.167
(1.00) 		0.00648
(1.00) 		1
(1.00) 		0.369
(1.00)
UPF3B 16 (6%) 232 0.735
(1.00) 		0.81
(1.00) 		0.395
(1.00) 		0.588
(1.00) 		0.0775
(1.00)
C9ORF102 16 (6%) 232 0.245
(1.00) 		0.35
(1.00) 		0.0343
(1.00) 		0.588
(1.00) 		0.568
(1.00)
RHBDD3 4 (2%) 244 0.587
(1.00) 		0.206
(1.00) 		0.961
(1.00) 		0.608
(1.00) 		0.577
(1.00)
C12ORF34 6 (2%) 242 0.542
(1.00) 		0.676
(1.00) 		0.897
(1.00) 		1
(1.00) 		0.193
(1.00)
FUT4 3 (1%) 245 0.87
(1.00) 		0.837
(1.00) 		0.0165
(1.00) 		0.271
(1.00) 		0.564
(1.00)
C7ORF60 10 (4%) 238 0.31
(1.00) 		0.136
(1.00) 		0.707
(1.00) 		0.318
(1.00) 		0.732
(1.00)
GYPB 5 (2%) 243 0.583
(1.00) 		0.843
(1.00) 		0.149
(1.00) 		0.168
(1.00) 		1
(1.00)
NHSL2 12 (5%) 236 0.992
(1.00) 		0.506
(1.00) 		0.0105
(1.00) 		0.756
(1.00) 		1
(1.00)
OR4K2 11 (4%) 237 0.304
(1.00) 		0.241
(1.00) 		0.00658
(1.00) 		1
(1.00) 		0.499
(1.00)
ZRANB3 8 (3%) 240 0.325
(1.00) 		0.839
(1.00) 		0.000987
(0.593) 		0.451
(1.00) 		0.452
(1.00)
KIF26B 19 (8%) 229 0.768
(1.00) 		0.403
(1.00) 		0.054
(1.00) 		0.46
(1.00) 		0.294
(1.00)
ZNF263 8 (3%) 240 0.452
(1.00) 		0.219
(1.00) 		0.809
(1.00) 		1
(1.00) 		0.22
(1.00)
DCAF4 4 (2%) 244 0.611
(1.00) 		0.0779
(1.00) 		0.328
(1.00) 		1
(1.00) 		1
(1.00)
PSMG4 5 (2%) 243 0.619
(1.00) 		0.778
(1.00) 		0.000441
(0.267) 		0.663
(1.00) 		0.327
(1.00)
TWF1 8 (3%) 240 0.437
(1.00) 		0.888
(1.00) 		0.205
(1.00) 		0.27
(1.00) 		1
(1.00)
OR52I2 8 (3%) 240 0.731
(1.00) 		0.559
(1.00) 		0.0802
(1.00) 		0.451
(1.00) 		0.452
(1.00)
SERHL2 6 (2%) 242 0.464
(1.00) 		0.666
(1.00) 		0.897
(1.00) 		0.185
(1.00) 		0.667
(1.00)
UBE2QL1 5 (2%) 243 0.753
(1.00) 		0.163
(1.00) 		0.933
(1.00) 		0.342
(1.00) 		1
(1.00)
ZNF649 14 (6%) 234 0.246
(1.00) 		0.288
(1.00) 		0.182
(1.00) 		0.777
(1.00) 		1
(1.00)
CHEK2 13 (5%) 235 0.891
(1.00) 		0.0163
(1.00) 		0.0307
(1.00) 		1
(1.00) 		0.352
(1.00)
IGFBP7 6 (2%) 242 0.406
(1.00) 		0.659
(1.00) 		0.228
(1.00) 		0.667
(1.00) 		0.667
(1.00)
OR5D13 10 (4%) 238 0.895
(1.00) 		0.741
(1.00) 		0.188
(1.00) 		0.318
(1.00) 		0.468
(1.00)
CSDE1 21 (8%) 227 0.802
(1.00) 		0.294
(1.00) 		0.0435
(1.00) 		1
(1.00) 		0.452
(1.00)
HLA-B 4 (2%) 244 0.523
(1.00) 		0.52
(1.00) 		0.078
(1.00) 		0.302
(1.00) 		0.303
(1.00)
OR4D2 3 (1%) 245 0.648
(1.00) 		0.693
(1.00) 		0.981
(1.00) 		0.271
(1.00) 		0.564
(1.00)
FMR1 16 (6%) 232 0.304
(1.00) 		0.643
(1.00) 		0.0688
(1.00) 		0.588
(1.00) 		0.0775
(1.00)
CNPY1 7 (3%) 241 0.449
(1.00) 		0.18
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.677
(1.00)
HIST1H2AG 7 (3%) 241 0.542
(1.00) 		0.416
(1.00) 		0.991
(1.00) 		0.0485
(1.00) 		1
(1.00)
CTXN3 6 (2%) 242 0.512
(1.00) 		0.794
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.193
(1.00)
OR4A15 13 (5%) 235 0.213
(1.00) 		0.167
(1.00) 		0.00219
(1.00) 		1
(1.00) 		0.756
(1.00)
CABP1 8 (3%) 240 0.319
(1.00) 		0.285
(1.00) 		0.809
(1.00) 		0.719
(1.00) 		0.452
(1.00)
TXNDC8 6 (2%) 242 0.439
(1.00) 		0.46
(1.00) 		0.32
(1.00) 		0.667
(1.00) 		1
(1.00)
FAM122A 6 (2%) 242 0.599
(1.00) 		0.936
(1.00) 		0.228
(1.00) 		0.415
(1.00) 		0.667
(1.00)
OR5AS1 10 (4%) 238 0.675
(1.00) 		0.503
(1.00) 		0.396
(1.00) 		0.501
(1.00) 		0.732
(1.00)
ZNF334 17 (7%) 231 0.95
(1.00) 		0.0232
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.415
(1.00)
C12ORF4 13 (5%) 235 0.287
(1.00) 		0.169
(1.00) 		0.00259
(1.00) 		1
(1.00) 		0.756
(1.00)
GNB2 6 (2%) 242 0.556
(1.00) 		0.388
(1.00) 		0.228
(1.00) 		0.667
(1.00) 		1
(1.00)
CABLES1 6 (2%) 242 0.425
(1.00) 		0.11
(1.00) 		0.897
(1.00) 		1
(1.00) 		1
(1.00)
KLHL8 12 (5%) 236 0.362
(1.00) 		0.504
(1.00) 		0.404
(1.00) 		1
(1.00) 		1
(1.00)
LOC642587 7 (3%) 241 0.679
(1.00) 		0.548
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.677
(1.00)
RAB3GAP1 16 (6%) 232 0.98
(1.00) 		0.596
(1.00) 		0.35
(1.00) 		1
(1.00) 		0.773
(1.00)
PAPD4 13 (5%) 235 0.982
(1.00) 		0.181
(1.00) 		0.962
(1.00) 		0.378
(1.00) 		0.0492
(1.00)
DAPP1 8 (3%) 240 0.568
(1.00) 		0.462
(1.00) 		0.343
(1.00) 		0.719
(1.00) 		0.688
(1.00)
DST 39 (16%) 209 0.467
(1.00) 		0.655
(1.00) 		0.301
(1.00) 		0.464
(1.00) 		0.563
(1.00)
HHIPL1 6 (2%) 242 0.679
(1.00) 		0.892
(1.00) 		0.32
(1.00) 		0.415
(1.00) 		0.667
(1.00)
LUC7L2 8 (3%) 240 0.332
(1.00) 		0.728
(1.00) 		0.343
(1.00) 		0.27
(1.00) 		0.452
(1.00)
MAP3K1 21 (8%) 227 0.0962
(1.00) 		0.813
(1.00) 		0.2
(1.00) 		1
(1.00) 		0.452
(1.00)
PPM1N 7 (3%) 241 0.355
(1.00) 		0.79
(1.00) 		0.294
(1.00) 		1
(1.00) 		1
(1.00)
ZNF879 13 (5%) 235 0.34
(1.00) 		0.0926
(1.00) 		0.4
(1.00) 		1
(1.00) 		1
(1.00)
TAF1 35 (14%) 213 0.231
(1.00) 		0.837
(1.00) 		0.0158
(1.00) 		0.448
(1.00) 		0.841
(1.00)
ZNF645 10 (4%) 238 0.353
(1.00) 		0.879
(1.00) 		0.0527
(1.00) 		1
(1.00) 		0.293
(1.00)
KCNH2 10 (4%) 238 0.432
(1.00) 		0.597
(1.00) 		0.338
(1.00) 		0.0959
(1.00) 		0.143
(1.00)
XPA 7 (3%) 241 0.169
(1.00) 		0.9
(1.00) 		0.981
(1.00) 		0.236
(1.00) 		0.092
(1.00)
ZNF449 12 (5%) 236 0.355
(1.00) 		0.95
(1.00) 		0.655
(1.00) 		0.552
(1.00) 		0.52
(1.00)
EDN1 4 (2%) 244 0.729
(1.00) 		0.741
(1.00) 		0.961
(1.00) 		0.608
(1.00) 		1
(1.00)
GIPC2 9 (4%) 239 0.851
(1.00) 		0.042
(1.00) 		0.376
(1.00) 		0.497
(1.00) 		0.709
(1.00)
C14ORF118 15 (6%) 233 0.268
(1.00) 		0.0138
(1.00) 		0.369
(1.00) 		0.589
(1.00) 		0.766
(1.00)
IGFN1 13 (5%) 235 0.713
(1.00) 		0.307
(1.00) 		0.296
(1.00) 		0.378
(1.00) 		0.756
(1.00)
BRS3 15 (6%) 233 0.184
(1.00) 		0.133
(1.00) 		0.025
(1.00) 		0.4
(1.00) 		0.766
(1.00)
TBC1D12 9 (4%) 239 0.479
(1.00) 		0.604
(1.00) 		0.759
(1.00) 		1
(1.00) 		1
(1.00)
NFE2L3 12 (5%) 236 0.336
(1.00) 		0.656
(1.00) 		0.342
(1.00) 		0.115
(1.00) 		0.741
(1.00)
G3BP2 9 (4%) 239 0.401
(1.00) 		0.101
(1.00) 		0.000879
(0.529) 		0.497
(1.00) 		0.709
(1.00)
RRAS2 4 (2%) 244 0.752
(1.00) 		0.0717
(1.00) 		0.961
(1.00) 		0.608
(1.00) 		0.0639
(1.00)
CLIC2 10 (4%) 238 0.294
(1.00) 		0.855
(1.00) 		0.00231
(1.00) 		1
(1.00) 		0.732
(1.00)
OPRK1 7 (3%) 241 0.594
(1.00) 		0.542
(1.00) 		0.856
(1.00) 		0.694
(1.00) 		0.677
(1.00)
HIST1H2BD 6 (2%) 242 0.0836
(1.00) 		0.474
(1.00) 		0.897
(1.00) 		0.415
(1.00) 		1
(1.00)
OR8B8 7 (3%) 241 0.524
(1.00) 		0.0339
(1.00) 		0.294
(1.00) 		0.428
(1.00) 		1
(1.00)
SHB 6 (2%) 242 0.484
(1.00) 		0.716
(1.00) 		0.996
(1.00) 		1
(1.00) 		0.667
(1.00)
SOS1 12 (5%) 236 0.301
(1.00) 		0.0904
(1.00) 		0.6
(1.00) 		0.552
(1.00) 		0.52
(1.00)
'PTEN MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.44e-19 (Chi-square test), Q value = 3.3e-16

Table S1.  Gene #2: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 182 3 8 2 5 4 44
PTEN MUTATED 146 2 6 1 4 1 1
PTEN WILD-TYPE 36 1 2 1 1 3 43

Figure S1.  Get High-res Image Gene #2: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'CTNNB1 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.04e-05 (Chi-square test), Q value = 0.0064

Table S2.  Gene #5: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 182 3 8 2 5 4 44
CTNNB1 MUTATED 69 1 2 2 0 0 0
CTNNB1 WILD-TYPE 113 2 6 0 5 4 44

Figure S2.  Get High-res Image Gene #5: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'KRAS MUTATION STATUS' versus 'AGE'

P value = 0.000274 (t-test), Q value = 0.17

Table S3.  Gene #6: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 248 63.1 (11.1)
KRAS MUTATED 53 58.8 (8.7)
KRAS WILD-TYPE 195 64.3 (11.4)

Figure S3.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'TP53 MUTATION STATUS' versus 'AGE'

P value = 6.15e-06 (t-test), Q value = 0.0038

Table S4.  Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 248 63.1 (11.1)
TP53 MUTATED 69 67.9 (9.4)
TP53 WILD-TYPE 179 61.3 (11.2)

Figure S4.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.98e-23 (Chi-square test), Q value = 2.4e-20

Table S5.  Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 182 3 8 2 5 4 44
TP53 MUTATED 23 0 0 0 4 3 39
TP53 WILD-TYPE 159 3 8 2 1 1 5

Figure S5.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'TP53 MUTATION STATUS' versus 'NEOADJUVANT.THERAPY'

P value = 6.08e-05 (Fisher's exact test), Q value = 0.037

Table S6.  Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'NEOADJUVANT.THERAPY'

nPatients NO YES
ALL 68 180
TP53 MUTATED 32 37
TP53 WILD-TYPE 36 143

Figure S6.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'NEOADJUVANT.THERAPY'

'SAP30 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.34e-08 (Chi-square test), Q value = 8.2e-06

Table S7.  Gene #55: 'SAP30 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 182 3 8 2 5 4 44
SAP30 MUTATED 2 0 0 0 2 0 0
SAP30 WILD-TYPE 180 3 8 2 3 4 44

Figure S7.  Get High-res Image Gene #55: 'SAP30 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'ZNF69 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000147 (Chi-square test), Q value = 0.089

Table S8.  Gene #89: 'ZNF69 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 182 3 8 2 5 4 44
ZNF69 MUTATED 5 0 0 0 2 0 0
ZNF69 WILD-TYPE 177 3 8 2 3 4 44

Figure S8.  Get High-res Image Gene #89: 'ZNF69 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'ANKRD31 MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.87e-05 (Chi-square test), Q value = 0.03

Table S9.  Gene #96: 'ANKRD31 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 182 3 8 2 5 4 44
ANKRD31 MUTATED 12 1 1 0 3 0 0
ANKRD31 WILD-TYPE 170 2 7 2 2 4 44

Figure S9.  Get High-res Image Gene #96: 'ANKRD31 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

  • Clinical data file = UCEC.clin.merged.picked.txt

  • Number of patients = 248

  • Number of significantly mutated genes = 123

  • Number of selected clinical features = 5

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

Survival analysis

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

Student's t-test analysis

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

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

Q value calculation

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

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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