Correlation between gene mutation status and selected clinical features
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.

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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