Colon/Rectal Adenocarcinoma: Correlation between gene mutation status and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 209 genes and 8 molecular subtypes across 224 patients, 22 significant findings detected with P value < 0.05 and Q value < 0.25.

  • FBXW7 mutation correlated to 'CN_CNMF'.

  • BRAF mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • TP53 mutation correlated to 'CN_CNMF'.

  • FAT4 mutation correlated to 'CN_CNMF'.

  • CDH2 mutation correlated to 'MRNA_CNMF'.

  • FLG mutation correlated to 'MRNA_CNMF'.

  • DNAH5 mutation correlated to 'CN_CNMF'.

  • TMEM132D mutation correlated to 'MRNA_CNMF'.

  • GRIA1 mutation correlated to 'RPPA_CHIERARCHICAL'.

  • ANK2 mutation correlated to 'MRNA_CHIERARCHICAL'.

  • ZC3H13 mutation correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • DOCK2 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • CDH10 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • SYNE1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • ZNF585A mutation correlated to 'RPPA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 209 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 22 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test
BRAF 22 (10%) 202 1.37e-06
(0.00191) 		1.88e-07
(0.000262) 		4.17e-05
(0.0578) 		0.651
(1.00) 		0.0155
(1.00) 		0.6
(1.00) 		1
(1.00)
SYNE1 47 (21%) 177 3.76e-05
(0.0523) 		9.65e-06
(0.0134) 		1.63e-06
(0.00227) 		1
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.367
(1.00) 		0.0326
(1.00)
ZC3H13 21 (9%) 203 0.000463
(0.633) 		7.69e-05
(0.106) 		8.41e-05
(0.116) 		0.116
(1.00) 		0.27
(1.00) 		1
(1.00) 		0.306
(1.00)
DOCK2 21 (9%) 203 0.000159
(0.219) 		0.000416
(0.571) 		0.000138
(0.19) 		0.445
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.101
(1.00)
CDH10 14 (6%) 210 6.12e-05
(0.0848) 		0.00291
(1.00) 		0.000131
(0.18) 		0.395
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.257
(1.00)
FBXW7 38 (17%) 186 0.0217
(1.00) 		0.00968
(1.00) 		0.000122
(0.168) 		0.0468
(1.00) 		0.216
(1.00) 		0.356
(1.00) 		0.118
(1.00)
TP53 120 (54%) 104 0.000448
(0.614) 		0.00229
(1.00) 		7.28e-11
(1.02e-07) 		0.464
(1.00) 		0.727
(1.00) 		0.0252
(1.00) 		0.134
(1.00)
FAT4 39 (17%) 185 0.0154
(1.00) 		0.117
(1.00) 		6.63e-05
(0.0919) 		0.89
(1.00) 		0.0835
(1.00) 		0.635
(1.00) 		0.683
(1.00)
CDH2 16 (7%) 208 3.86e-05
(0.0536) 		0.00587
(1.00) 		0.00381
(1.00) 		0.213
(1.00) 		0.483
(1.00) 		0.41
(1.00) 		0.683
(1.00)
FLG 32 (14%) 192 3.08e-06
(0.00428) 		0.00083
(1.00) 		0.00376
(1.00) 		0.0553
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.74
(1.00)
DNAH5 34 (15%) 190 0.000239
(0.328) 		0.000915
(1.00) 		0.00013
(0.179) 		0.83
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.238
(1.00)
TMEM132D 19 (8%) 205 3.34e-05
(0.0465) 		0.00169
(1.00) 		0.00293
(1.00) 		0.0898
(1.00) 		0.0384
(1.00) 		1
(1.00) 		1
(1.00)
GRIA1 15 (7%) 209 0.0584
(1.00) 		0.31
(1.00) 		0.0104
(1.00) 		0.598
(1.00) 		1.09e-07
(0.000152) 		1
(1.00) 		0.0226
(1.00)
ANK2 30 (13%) 194 0.000803
(1.00) 		7.61e-05
(0.105) 		0.0015
(1.00) 		0.000819
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.0416
(1.00)
ZNF585A 10 (4%) 214 0.00278
(1.00) 		0.0485
(1.00) 		0.00451
(1.00) 		0.321
(1.00) 		3.69e-05
(0.0514) 		1
(1.00) 		0.0935
(1.00)
NRAS 20 (9%) 204 0.0344
(1.00) 		0.241
(1.00) 		0.274
(1.00) 		0.703
(1.00) 		0.883
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 33 (15%) 191 0.212
(1.00) 		0.783
(1.00) 		0.00048
(0.657) 		0.0341
(1.00) 		0.0618
(1.00) 		0.0853
(1.00) 		1
(1.00)
APC 160 (71%) 64 0.0181
(1.00) 		0.00811
(1.00) 		0.221
(1.00) 		0.642
(1.00) 		0.625
(1.00) 		0.689
(1.00) 		0.464
(1.00)
KRAS 96 (43%) 128 0.000502
(0.685) 		0.0982
(1.00) 		0.485
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.991
(1.00) 		0.0688
(1.00) 		0.735
(1.00)
SMAD4 26 (12%) 198 0.0254
(1.00) 		0.334
(1.00) 		0.0355
(1.00) 		0.89
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.846
(1.00)
FAM123B 25 (11%) 199 0.086
(1.00) 		0.0244
(1.00) 		0.00539
(1.00) 		0.504
(1.00) 		0.847
(1.00) 		1
(1.00) 		0.459
(1.00)
TTN 85 (38%) 139 0.00685
(1.00) 		0.0565
(1.00) 		0.00133
(1.00) 		0.657
(1.00) 		0.216
(1.00) 		0.148
(1.00) 		0.151
(1.00) 		0.927
(1.00)
SMAD2 15 (7%) 209 0.123
(1.00) 		0.512
(1.00) 		0.0393
(1.00) 		0.191
(1.00) 		0.229
(1.00) 		1
(1.00) 		0.711
(1.00)
TCF7L2 18 (8%) 206 1
(1.00) 		0.364
(1.00) 		0.417
(1.00) 		0.297
(1.00) 		0.472
(1.00) 		1
(1.00) 		0.23
(1.00)
KRTAP5-5 4 (2%) 220 0.356
(1.00) 		1
(1.00) 		0.48
(1.00) 		0.655
(1.00) 		0.144
(1.00) 		1
(1.00) 		1
(1.00)
ACVR1B 14 (6%) 210 0.119
(1.00) 		0.216
(1.00) 		0.0496
(1.00) 		0.321
(1.00) 		0.322
(1.00) 		0.435
(1.00) 		0.711
(1.00)
WBSCR17 19 (8%) 205 0.103
(1.00) 		0.303
(1.00) 		0.141
(1.00) 		0.333
(1.00) 		0.0439
(1.00) 		0.544
(1.00) 		0.618
(1.00)
PCDH9 22 (10%) 202 0.844
(1.00) 		0.585
(1.00) 		0.0495
(1.00) 		0.651
(1.00) 		0.359
(1.00) 		0.563
(1.00) 		1
(1.00)
LRP1B 39 (17%) 185 0.00343
(1.00) 		0.00478
(1.00) 		0.00332
(1.00) 		0.325
(1.00) 		0.0815
(1.00) 		1
(1.00) 		0.087
(1.00)
TNFRSF10C 6 (3%) 218 0.377
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.213
(1.00) 		0.057
(1.00) 		1
(1.00) 		1
(1.00)
MAP2K4 11 (5%) 213 0.0796
(1.00) 		0.49
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.545
(1.00)
KIAA1804 15 (7%) 209 0.237
(1.00) 		0.291
(1.00) 		0.0659
(1.00) 		0.475
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.736
(1.00)
NRXN1 20 (9%) 204 0.463
(1.00) 		0.322
(1.00) 		0.0843
(1.00) 		1
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.13
(1.00)
KLHL4 16 (7%) 208 0.0137
(1.00) 		0.0161
(1.00) 		0.00117
(1.00) 		0.164
(1.00) 		0.467
(1.00) 		0.41
(1.00) 		0.0126
(1.00)
SOX9 10 (4%) 214 0.139
(1.00) 		0.585
(1.00) 		0.00451
(1.00) 		0.655
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.584
(1.00)
PRDM9 16 (7%) 208 0.00531
(1.00) 		0.87
(1.00) 		0.0701
(1.00) 		0.333
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.255
(1.00)
PCBP1 6 (3%) 218 0.187
(1.00) 		0.222
(1.00) 		0.396
(1.00) 		1
(1.00) 		1
(1.00)
DMD 33 (15%) 191 0.0202
(1.00) 		0.0205
(1.00) 		0.0052
(1.00) 		0.362
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.156
(1.00)
CSMD1 26 (12%) 198 0.16
(1.00) 		0.124
(1.00) 		0.0523
(1.00) 		1
(1.00) 		0.0749
(1.00) 		0.369
(1.00) 		0.0581
(1.00) 		0.142
(1.00)
LIFR 18 (8%) 206 0.119
(1.00) 		0.635
(1.00) 		0.219
(1.00) 		0.703
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.064
(1.00)
OR6N1 10 (4%) 214 0.00204
(1.00) 		0.127
(1.00) 		0.013
(1.00) 		1
(1.00) 		0.0449
(1.00) 		0.304
(1.00) 		1
(1.00)
CCDC160 7 (3%) 217 0.0688
(1.00) 		0.477
(1.00) 		0.108
(1.00) 		0.171
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.0575
(1.00)
CNTN6 17 (8%) 207 0.162
(1.00) 		0.341
(1.00) 		0.0782
(1.00) 		0.152
(1.00) 		0.0499
(1.00) 		1
(1.00) 		0.322
(1.00)
CPXCR1 9 (4%) 215 0.00296
(1.00) 		0.153
(1.00) 		0.191
(1.00) 		0.655
(1.00) 		0.909
(1.00) 		0.304
(1.00) 		0.0285
(1.00)
SLITRK1 15 (7%) 209 0.517
(1.00) 		0.879
(1.00) 		0.159
(1.00) 		0.333
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.181
(1.00)
CNBD1 7 (3%) 217 0.768
(1.00) 		0.688
(1.00) 		0.293
(1.00) 		1
(1.00) 		0.406
(1.00)
CTNNB1 11 (5%) 213 0.672
(1.00) 		0.75
(1.00) 		0.048
(1.00) 		0.865
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.545
(1.00)
DKK2 6 (3%) 218 0.0358
(1.00) 		0.0109
(1.00) 		0.628
(1.00) 		0.152
(1.00) 		0.0353
(1.00) 		1
(1.00) 		1
(1.00)
ERBB4 18 (8%) 206 0.121
(1.00) 		0.553
(1.00) 		0.00631
(1.00) 		0.529
(1.00) 		0.464
(1.00) 		0.481
(1.00) 		0.76
(1.00)
ARID1A 21 (9%) 203 0.0239
(1.00) 		0.102
(1.00) 		0.0136
(1.00) 		0.338
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.064
(1.00)
KIAA1486 13 (6%) 211 0.361
(1.00) 		0.915
(1.00) 		0.306
(1.00) 		0.321
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.0638
(1.00)
ROBO1 18 (8%) 206 0.0053
(1.00) 		0.00861
(1.00) 		0.0221
(1.00) 		0.0325
(1.00) 		0.134
(1.00) 		0.502
(1.00) 		0.281
(1.00)
ZFHX4 24 (11%) 200 0.72
(1.00) 		0.332
(1.00) 		0.0166
(1.00) 		1
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.072
(1.00)
EPHA3 16 (7%) 208 0.000482
(0.658) 		0.00405
(1.00) 		0.214
(1.00) 		0.703
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.23
(1.00)
PRIM2 8 (4%) 216 0.277
(1.00) 		0.779
(1.00) 		0.889
(1.00) 		0.104
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.406
(1.00)
UBE2NL 7 (3%) 217 0.108
(1.00) 		0.446
(1.00) 		0.402
(1.00) 		0.06
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.351
(1.00)
ACVR2A 9 (4%) 215 0.00858
(1.00) 		0.443
(1.00) 		0.0325
(1.00) 		0.321
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.545
(1.00)
ADAM29 11 (5%) 213 0.451
(1.00) 		1
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.545
(1.00)
ATP10A 19 (8%) 205 0.0197
(1.00) 		0.101
(1.00) 		0.141
(1.00) 		0.0292
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.386
(1.00)
GABRA5 9 (4%) 215 0.487
(1.00) 		0.342
(1.00) 		0.756
(1.00) 		0.244
(1.00) 		0.456
(1.00)
NALCN 20 (9%) 204 0.0419
(1.00) 		0.101
(1.00) 		0.141
(1.00) 		0.823
(1.00) 		0.361
(1.00) 		1
(1.00) 		0.053
(1.00)
OTOL1 8 (4%) 216 0.132
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.274
(1.00) 		0.502
(1.00)
PTEN 7 (3%) 217 0.0222
(1.00) 		0.218
(1.00) 		0.0429
(1.00) 		0.777
(1.00) 		0.323
(1.00) 		0.244
(1.00) 		0.0575
(1.00)
SDK1 27 (12%) 197 0.0106
(1.00) 		0.000738
(1.00) 		0.24
(1.00) 		0.394
(1.00) 		0.755
(1.00) 		0.6
(1.00) 		1
(1.00)
TLL1 15 (7%) 209 0.0358
(1.00) 		0.631
(1.00) 		0.02
(1.00) 		0.164
(1.00) 		0.147
(1.00) 		0.359
(1.00) 		0.00952
(1.00)
TRPC4 17 (8%) 207 0.0053
(1.00) 		0.0217
(1.00) 		0.0139
(1.00) 		0.75
(1.00) 		0.0375
(1.00) 		0.481
(1.00) 		0.171
(1.00)
ATM 25 (11%) 199 0.00324
(1.00) 		0.0867
(1.00) 		0.000415
(0.569) 		0.34
(1.00) 		0.229
(1.00) 		0.6
(1.00) 		0.162
(1.00)
GPC6 10 (4%) 214 0.569
(1.00) 		0.316
(1.00) 		0.509
(1.00) 		0.264
(1.00) 		0.467
(1.00) 		1
(1.00) 		1
(1.00)
CDH8 14 (6%) 210 0.00127
(1.00) 		0.000535
(0.73) 		0.124
(1.00) 		0.473
(1.00) 		0.304
(1.00) 		1
(1.00) 		1
(1.00)
MGC26647 7 (3%) 217 0.287
(1.00) 		0.872
(1.00) 		0.0498
(1.00) 		0.81
(1.00) 		0.891
(1.00) 		1
(1.00) 		0.351
(1.00)
DKK4 7 (3%) 217 0.299
(1.00) 		0.125
(1.00) 		0.402
(1.00) 		0.833
(1.00) 		0.856
(1.00) 		1
(1.00) 		1
(1.00)
PTPRM 20 (9%) 204 0.0483
(1.00) 		0.00861
(1.00) 		0.00293
(1.00) 		0.333
(1.00) 		0.898
(1.00) 		0.523
(1.00) 		0.0381
(1.00)
AFF2 17 (8%) 207 0.0512
(1.00) 		0.0541
(1.00) 		0.201
(1.00) 		0.346
(1.00) 		0.00181
(1.00) 		0.481
(1.00) 		0.255
(1.00)
NCAM2 12 (5%) 212 0.0115
(1.00) 		0.313
(1.00) 		0.0617
(1.00) 		0.655
(1.00) 		0.118
(1.00) 		1
(1.00) 		0.0387
(1.00)
OR2M4 8 (4%) 216 0.0102
(1.00) 		0.254
(1.00) 		0.0382
(1.00) 		0.416
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.502
(1.00)
RYR2 29 (13%) 195 0.041
(1.00) 		0.0914
(1.00) 		0.0195
(1.00) 		0.157
(1.00) 		0.134
(1.00) 		0.6
(1.00) 		0.0755
(1.00)
CDH9 15 (7%) 209 0.135
(1.00) 		0.137
(1.00) 		0.0226
(1.00) 		0.549
(1.00) 		0.169
(1.00) 		1
(1.00) 		0.158
(1.00)
GRIK3 17 (8%) 207 0.00835
(1.00) 		0.00963
(1.00) 		0.196
(1.00) 		0.622
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.711
(1.00)
ELF3 6 (3%) 218 0.328
(1.00) 		0.125
(1.00) 		0.0514
(1.00) 		0.416
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.406
(1.00)
TRPS1 17 (8%) 207 0.01
(1.00) 		0.0792
(1.00) 		0.00133
(1.00) 		0.152
(1.00) 		0.1
(1.00) 		0.458
(1.00) 		0.354
(1.00)
FAM133A 7 (3%) 217 0.333
(1.00) 		0.872
(1.00) 		0.0183
(1.00) 		0.171
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.456
(1.00)
IL1RAPL2 10 (4%) 214 0.356
(1.00) 		0.75
(1.00) 		0.0473
(1.00) 		0.213
(1.00) 		0.651
(1.00) 		0.0412
(1.00) 		1
(1.00)
CCBP2 10 (4%) 214 0.154
(1.00) 		0.316
(1.00) 		0.623
(1.00) 		0.488
(1.00) 		0.485
(1.00) 		1
(1.00) 		0.162
(1.00)
OPCML 10 (4%) 214 0.335
(1.00) 		0.347
(1.00) 		0.543
(1.00) 		0.213
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.0935
(1.00)
CDH18 13 (6%) 211 0.00184
(1.00) 		0.313
(1.00) 		0.0984
(1.00) 		0.0354
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.62
(1.00)
OR2L13 10 (4%) 214 0.165
(1.00) 		0.443
(1.00) 		0.0275
(1.00) 		0.116
(1.00) 		0.817
(1.00) 		1
(1.00) 		1
(1.00)
LRRN3 10 (4%) 214 0.00253
(1.00) 		0.0952
(1.00) 		0.446
(1.00) 		0.0183
(1.00) 		0.82
(1.00) 		0.274
(1.00) 		0.502
(1.00)
BAI3 18 (8%) 206 0.00782
(1.00) 		0.206
(1.00) 		0.423
(1.00) 		0.75
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.255
(1.00)
MGC42105 11 (5%) 213 0.00161
(1.00) 		0.197
(1.00) 		0.147
(1.00) 		0.395
(1.00) 		0.015
(1.00) 		1
(1.00) 		1
(1.00)
TXNDC3 11 (5%) 213 0.00292
(1.00) 		0.0485
(1.00) 		0.0125
(1.00) 		0.777
(1.00) 		0.00686
(1.00) 		1
(1.00) 		0.00311
(1.00)
LPPR4 13 (6%) 211 0.0835
(1.00) 		0.00634
(1.00) 		0.0342
(1.00) 		0.549
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.653
(1.00)
UNC13C 17 (8%) 207 0.00812
(1.00) 		0.137
(1.00) 		0.0257
(1.00) 		0.073
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.255
(1.00)
SCN7A 15 (7%) 209 0.000715
(0.975) 		0.0293
(1.00) 		0.0492
(1.00) 		0.167
(1.00) 		0.26
(1.00) 		1
(1.00) 		0.205
(1.00)
ACOT4 3 (1%) 221 0.298
(1.00) 		0.288
(1.00) 		0.829
(1.00) 		1
(1.00) 		1
(1.00)
GGT1 3 (1%) 221 0.254
(1.00) 		1
(1.00) 		1
(1.00)
ING1 6 (3%) 218 0.294
(1.00) 		0.71
(1.00) 		0.628
(1.00) 		1
(1.00) 		0.406
(1.00)
PCDHA10 10 (4%) 214 0.0819
(1.00) 		0.258
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.545
(1.00)
ZNF208 11 (5%) 213 0.186
(1.00) 		0.915
(1.00) 		0.249
(1.00) 		0.171
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.114
(1.00)
CRTC1 6 (3%) 218 0.123
(1.00) 		0.0422
(1.00) 		0.837
(1.00) 		0.104
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.406
(1.00)
FAM5C 13 (6%) 211 0.459
(1.00) 		0.712
(1.00) 		0.0186
(1.00) 		0.101
(1.00) 		0.0808
(1.00) 		0.0711
(1.00) 		0.653
(1.00)
GUCY1A3 12 (5%) 212 0.395
(1.00) 		0.197
(1.00) 		0.0311
(1.00) 		0.777
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.584
(1.00)
FAM22F 9 (4%) 215 0.691
(1.00) 		0.731
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.828
(1.00) 		1
(1.00) 		1
(1.00)
CHRDL1 11 (5%) 213 0.168
(1.00) 		0.648
(1.00) 		0.472
(1.00) 		0.126
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.584
(1.00)
EDNRB 10 (4%) 214 0.0668
(1.00) 		0.912
(1.00) 		0.757
(1.00) 		0.488
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.545
(1.00)
IFT80 10 (4%) 214 0.0592
(1.00) 		0.153
(1.00) 		0.254
(1.00) 		0.304
(1.00) 		0.162
(1.00)
CASP14 8 (4%) 216 1
(1.00) 		0.333
(1.00) 		0.889
(1.00) 		0.735
(1.00) 		0.732
(1.00) 		0.274
(1.00) 		1
(1.00)
LASS3 9 (4%) 215 0.00364
(1.00) 		0.182
(1.00) 		0.104
(1.00) 		0.0859
(1.00) 		0.69
(1.00) 		1
(1.00) 		0.0747
(1.00)
P2RY10 7 (3%) 217 0.661
(1.00) 		0.382
(1.00) 		0.402
(1.00) 		0.598
(1.00) 		0.485
(1.00) 		1
(1.00) 		1
(1.00)
CNTN1 14 (6%) 210 0.0177
(1.00) 		0.0609
(1.00) 		0.00405
(1.00) 		0.876
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.181
(1.00)
ISL1 8 (4%) 216 0.304
(1.00) 		0.443
(1.00) 		0.435
(1.00) 		0.213
(1.00) 		0.105
(1.00) 		1
(1.00) 		0.502
(1.00)
ARID2 15 (7%) 209 0.161
(1.00) 		0.132
(1.00) 		0.0254
(1.00) 		0.257
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.0638
(1.00)
EIF4A2 5 (2%) 219 0.548
(1.00) 		0.512
(1.00) 		0.73
(1.00) 		0.598
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.141
(1.00)
OR51V1 9 (4%) 215 0.00273
(1.00) 		0.00886
(1.00) 		0.0016
(1.00) 		0.342
(1.00) 		0.0515
(1.00) 		1
(1.00) 		0.545
(1.00)
CDH11 14 (6%) 210 0.0683
(1.00) 		0.247
(1.00) 		0.0175
(1.00) 		1
(1.00) 		0.713
(1.00) 		0.385
(1.00) 		1
(1.00)
CHST9 8 (4%) 216 0.0121
(1.00) 		0.443
(1.00) 		0.0706
(1.00) 		1
(1.00) 		0.456
(1.00)
HTR3B 6 (3%) 218 0.131
(1.00) 		0.736
(1.00) 		0.628
(1.00) 		0.06
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.351
(1.00)
LRRIQ3 10 (4%) 214 0.176
(1.00) 		0.231
(1.00) 		0.157
(1.00) 		0.503
(1.00) 		0.0187
(1.00) 		1
(1.00) 		0.114
(1.00)
HCN1 10 (4%) 214 0.287
(1.00) 		0.382
(1.00) 		0.0201
(1.00) 		0.326
(1.00) 		0.23
(1.00) 		1
(1.00) 		1
(1.00)
CHRM2 10 (4%) 214 0.0935
(1.00) 		0.443
(1.00) 		0.115
(1.00) 		1
(1.00) 		0.732
(1.00) 		1
(1.00) 		0.545
(1.00)
CSMD3 28 (12%) 196 0.0072
(1.00) 		0.00467
(1.00) 		0.00457
(1.00) 		0.0154
(1.00) 		0.133
(1.00) 		0.6
(1.00) 		0.0587
(1.00)
DCAF4L2 11 (5%) 213 0.00364
(1.00) 		0.00609
(1.00) 		0.027
(1.00) 		0.304
(1.00) 		0.545
(1.00)
DACH2 12 (5%) 212 0.134
(1.00) 		0.29
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.114
(1.00)
PCDH11X 14 (6%) 210 0.0194
(1.00) 		0.512
(1.00) 		0.107
(1.00) 		0.104
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.181
(1.00)
KCNA4 12 (5%) 212 0.113
(1.00) 		0.0186
(1.00) 		0.00254
(1.00) 		0.0183
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.584
(1.00)
DPP10 13 (6%) 211 0.00138
(1.00) 		0.49
(1.00) 		0.0895
(1.00) 		0.105
(1.00) 		0.322
(1.00) 		0.385
(1.00) 		0.158
(1.00)
EVC2 17 (8%) 207 0.00556
(1.00) 		0.00861
(1.00) 		0.0383
(1.00) 		0.334
(1.00) 		0.0684
(1.00) 		1
(1.00) 		0.711
(1.00)
C15ORF2 12 (5%) 212 0.0187
(1.00) 		0.443
(1.00) 		0.166
(1.00) 		0.213
(1.00) 		0.0786
(1.00) 		0.304
(1.00) 		0.0492
(1.00)
NLRP5 12 (5%) 212 0.172
(1.00) 		1
(1.00) 		0.0649
(1.00) 		0.0657
(1.00) 		0.124
(1.00) 		1
(1.00) 		0.584
(1.00)
BTNL8 3 (1%) 221 0.298
(1.00) 		0.288
(1.00) 		0.254
(1.00) 		0.283
(1.00) 		0.636
(1.00) 		1
(1.00) 		1
(1.00)
KLK2 3 (1%) 221 0.471
(1.00) 		0.288
(1.00) 		0.829
(1.00) 		1
(1.00)
LUZP2 6 (3%) 218 0.0794
(1.00) 		0.183
(1.00) 		0.175
(1.00) 		1
(1.00) 		0.016
(1.00) 		1
(1.00) 		1
(1.00)
NXF5 7 (3%) 217 0.257
(1.00) 		0.861
(1.00) 		0.425
(1.00) 		0.777
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.0421
(1.00)
PCDHB5 14 (6%) 210 0.264
(1.00) 		0.496
(1.00) 		0.0582
(1.00) 		0.423
(1.00) 		0.0458
(1.00) 		0.385
(1.00) 		0.653
(1.00)
LOXL2 9 (4%) 215 0.674
(1.00) 		0.698
(1.00) 		0.191
(1.00) 		0.549
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.32
(1.00)
UBQLNL 5 (2%) 219 0.121
(1.00) 		0.208
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MYO1B 13 (6%) 211 0.00981
(1.00) 		0.00115
(1.00) 		0.00752
(1.00) 		0.191
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.653
(1.00)
SPATA17 9 (4%) 215 0.111
(1.00) 		0.479
(1.00) 		0.0519
(1.00) 		0.833
(1.00) 		0.221
(1.00) 		1
(1.00) 		1
(1.00)
RIMS1 15 (7%) 209 0.254
(1.00) 		0.408
(1.00) 		0.00135
(1.00) 		0.297
(1.00) 		0.27
(1.00) 		0.458
(1.00) 		0.736
(1.00)
COL12A1 21 (9%) 203 0.0106
(1.00) 		0.398
(1.00) 		0.0451
(1.00) 		0.876
(1.00) 		0.286
(1.00) 		0.523
(1.00) 		0.0753
(1.00)
JAKMIP2 13 (6%) 211 0.0168
(1.00) 		0.247
(1.00) 		0.0855
(1.00) 		0.257
(1.00) 		0.462
(1.00) 		0.385
(1.00) 		0.158
(1.00)
EPHA5 13 (6%) 211 0.0675
(1.00) 		0.132
(1.00) 		0.0666
(1.00) 		0.434
(1.00) 		0.885
(1.00) 		1
(1.00) 		0.653
(1.00)
ODZ1 22 (10%) 202 0.396
(1.00) 		0.272
(1.00) 		0.0474
(1.00) 		0.39
(1.00) 		0.888
(1.00) 		0.204
(1.00) 		0.669
(1.00)
POSTN 11 (5%) 213 0.0215
(1.00) 		0.0882
(1.00) 		0.272
(1.00) 		0.283
(1.00) 		0.669
(1.00) 		1
(1.00) 		1
(1.00)
ZCWPW2 7 (3%) 217 0.36
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.116
(1.00) 		1
(1.00) 		0.104
(1.00)
ZEB2 15 (7%) 209 0.0434
(1.00) 		0.87
(1.00) 		0.164
(1.00) 		0.586
(1.00) 		0.696
(1.00) 		0.385
(1.00) 		0.653
(1.00)
TUSC3 7 (3%) 217 0.00678
(1.00) 		0.153
(1.00) 		0.04
(1.00) 		0.598
(1.00) 		0.0277
(1.00) 		1
(1.00) 		0.00375
(1.00)
CACNG7 6 (3%) 218 0.649
(1.00) 		0.23
(1.00) 		0.363
(1.00) 		0.321
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.213
(1.00)
RWDD2B 8 (4%) 216 0.0527
(1.00) 		0.443
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.00375
(1.00)
SLC25A13 7 (3%) 217 0.148
(1.00) 		0.597
(1.00) 		0.425
(1.00) 		0.0859
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.0421
(1.00)
DPF2 4 (2%) 220 0.471
(1.00) 		0.288
(1.00) 		0.381
(1.00) 		0.171
(1.00) 		0.122
(1.00) 		1
(1.00) 		0.141
(1.00)
PCDH10 17 (8%) 207 0.0996
(1.00) 		0.0505
(1.00) 		0.0139
(1.00) 		0.876
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.23
(1.00)
CDH12 13 (6%) 211 0.00538
(1.00) 		0.132
(1.00) 		0.0874
(1.00) 		0.0616
(1.00) 		0.279
(1.00) 		1
(1.00) 		0.00946
(1.00)
MCF2 12 (5%) 212 0.0885
(1.00) 		0.056
(1.00) 		0.263
(1.00) 		0.326
(1.00) 		0.246
(1.00) 		1
(1.00) 		0.135
(1.00)
NCKAP5 15 (7%) 209 0.0261
(1.00) 		0.018
(1.00) 		0.131
(1.00) 		0.0292
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.711
(1.00)
RIMS2 13 (6%) 211 0.00189
(1.00) 		0.368
(1.00) 		0.000306
(0.42) 		0.175
(1.00) 		0.118
(1.00) 		1
(1.00) 		0.653
(1.00)
ATP7A 6 (3%) 218 0.704
(1.00) 		0.819
(1.00) 		0.917
(1.00) 		0.655
(1.00) 		0.415
(1.00) 		1
(1.00) 		1
(1.00)
TPTE 12 (5%) 212 0.0249
(1.00) 		0.231
(1.00) 		0.000369
(0.507) 		0.655
(1.00) 		0.0873
(1.00) 		1
(1.00) 		0.62
(1.00)
OR8B4 6 (3%) 218 0.0688
(1.00) 		0.405
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.351
(1.00)
SFMBT2 13 (6%) 211 0.552
(1.00) 		0.247
(1.00) 		0.387
(1.00) 		0.655
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.683
(1.00)
FLRT2 13 (6%) 211 0.149
(1.00) 		0.74
(1.00) 		0.019
(1.00) 		0.191
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.135
(1.00)
BCHE 9 (4%) 215 0.057
(1.00) 		0.259
(1.00) 		0.314
(1.00) 		1
(1.00) 		0.518
(1.00) 		1
(1.00) 		1
(1.00)
C8B 10 (4%) 214 0.0748
(1.00) 		0.259
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.713
(1.00) 		1
(1.00) 		1
(1.00)
FREM2 23 (10%) 201 0.179
(1.00) 		0.413
(1.00) 		0.299
(1.00) 		0.372
(1.00) 		0.418
(1.00) 		0.6
(1.00) 		0.409
(1.00)
ZNF167 7 (3%) 217 0.287
(1.00) 		0.688
(1.00) 		0.0498
(1.00) 		0.777
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.406
(1.00)
GABRG1 8 (4%) 216 0.562
(1.00) 		0.892
(1.00) 		0.459
(1.00) 		0.213
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.0747
(1.00)
SAT1 4 (2%) 220 0.00282
(1.00) 		0.0612
(1.00) 		0.0742
(1.00) 		0.777
(1.00) 		0.635
(1.00) 		1
(1.00) 		1
(1.00)
CHD4 17 (8%) 207 0.0106
(1.00) 		0.058
(1.00) 		0.000862
(1.00) 		0.338
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.0101
(1.00)
PCDHB2 14 (6%) 210 0.012
(1.00) 		0.00956
(1.00) 		0.0175
(1.00) 		0.735
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.653
(1.00)
TMTC1 13 (6%) 211 0.181
(1.00) 		0.056
(1.00) 		0.0147
(1.00) 		0.101
(1.00) 		0.842
(1.00) 		0.385
(1.00) 		0.158
(1.00)
SH3GL3 8 (4%) 216 0.108
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.0476
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.133
(1.00)
ZFPM2 6 (3%) 218 0.024
(1.00) 		0.736
(1.00) 		0.541
(1.00) 		0.321
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.0549
(1.00)
CACNG3 8 (4%) 216 0.0187
(1.00) 		0.0952
(1.00) 		0.00923
(1.00) 		0.0149
(1.00) 		0.458
(1.00) 		0.274
(1.00) 		0.0747
(1.00)
POTEB 8 (4%) 216 0.309
(1.00) 		1
(1.00) 		0.287
(1.00) 		1
(1.00) 		1
(1.00)
GRIN2A 19 (8%) 205 0.413
(1.00) 		0.462
(1.00) 		0.0439
(1.00) 		0.408
(1.00) 		0.827
(1.00) 		0.481
(1.00) 		0.76
(1.00)
NRXN3 17 (8%) 207 0.000473
(0.647) 		0.0656
(1.00) 		0.00293
(1.00) 		1
(1.00) 		0.0375
(1.00) 		1
(1.00) 		0.736
(1.00)
OR7C1 6 (3%) 218 0.131
(1.00) 		0.0109
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.406
(1.00)
SPATA8 3 (1%) 221 0.312
(1.00) 		1
(1.00) 		0.104
(1.00)
OR2M2 6 (3%) 218 0.808
(1.00) 		1
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.351
(1.00)
SORCS1 15 (7%) 209 0.243
(1.00) 		0.217
(1.00) 		0.131
(1.00) 		0.876
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.205
(1.00)
IL18R1 10 (4%) 214 0.0398
(1.00) 		0.101
(1.00) 		0.254
(1.00) 		0.321
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.114
(1.00)
DPY19L1 5 (2%) 219 0.0102
(1.00) 		0.324
(1.00) 		0.194
(1.00) 		0.104
(1.00) 		0.022
(1.00) 		1
(1.00) 		0.292
(1.00)
C16ORF45 3 (1%) 221 0.139
(1.00) 		0.588
(1.00) 		0.108
(1.00) 		1
(1.00) 		1
(1.00)
INHBA 9 (4%) 215 0.005
(1.00) 		0.0952
(1.00) 		0.0706
(1.00) 		0.025
(1.00) 		0.0575
(1.00)
MIER3 11 (5%) 213 0.000183
(0.252) 		0.0174
(1.00) 		0.00207
(1.00) 		0.735
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.62
(1.00)
TMPRSS13 4 (2%) 220 0.388
(1.00) 		0.403
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.292
(1.00)
FSTL5 11 (5%) 213 0.0586
(1.00) 		0.197
(1.00) 		0.0316
(1.00) 		0.0823
(1.00) 		0.036
(1.00) 		1
(1.00) 		0.193
(1.00)
DOK5 6 (3%) 218 0.894
(1.00) 		0.552
(1.00) 		0.628
(1.00) 		0.424
(1.00) 		0.485
(1.00) 		1
(1.00) 		0.213
(1.00)
ZNF99 11 (5%) 213 0.052
(1.00) 		0.231
(1.00) 		0.0153
(1.00) 		0.104
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.0387
(1.00)
GML 6 (3%) 218 0.453
(1.00) 		0.153
(1.00) 		0.628
(1.00) 		1
(1.00) 		1
(1.00)
B2M 5 (2%) 219 0.0423
(1.00) 		0.11
(1.00) 		0.0452
(1.00) 		0.777
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.0288
(1.00)
PPP2R2B 3 (1%) 221 0.471
(1.00) 		0.288
(1.00) 		0.445
(1.00) 		1
(1.00) 		0.228
(1.00)
LRTM1 7 (3%) 217 0.0934
(1.00) 		0.218
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.351
(1.00)
OR10G9 6 (3%) 218 0.241
(1.00) 		0.324
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.351
(1.00)
ERBB3 14 (6%) 210 0.147
(1.00) 		0.09
(1.00) 		0.124
(1.00) 		0.703
(1.00) 		0.741
(1.00) 		1
(1.00) 		0.158
(1.00)
PSG8 8 (4%) 216 0.894
(1.00) 		0.477
(1.00) 		0.107
(1.00) 		0.244
(1.00) 		0.249
(1.00)
SYT16 9 (4%) 215 0.0778
(1.00) 		0.042
(1.00) 		0.182
(1.00) 		0.0262
(1.00) 		0.483
(1.00) 		0.304
(1.00) 		0.545
(1.00)
LPHN3 13 (6%) 211 0.00327
(1.00) 		0.0792
(1.00) 		0.387
(1.00) 		0.0042
(1.00) 		0.23
(1.00) 		1
(1.00) 		0.135
(1.00)
LRP2 35 (16%) 189 0.00219
(1.00) 		0.0155
(1.00) 		0.0014
(1.00) 		0.649
(1.00) 		0.569
(1.00) 		0.342
(1.00) 		0.277
(1.00)
SOHLH2 9 (4%) 215 0.86
(1.00) 		0.042
(1.00) 		0.327
(1.00) 		0.171
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.502
(1.00)
ZIM3 9 (4%) 215 0.0665
(1.00) 		0.892
(1.00) 		0.119
(1.00) 		0.00346
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.0285
(1.00)
DSEL 14 (6%) 210 0.0139
(1.00) 		0.217
(1.00) 		0.00117
(1.00) 		0.395
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.158
(1.00)
RNASE11 5 (2%) 219 0.814
(1.00) 		0.71
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.0177
(1.00)
MDGA2 10 (4%) 214 0.0217
(1.00) 		0.03
(1.00) 		0.0201
(1.00) 		0.503
(1.00) 		0.829
(1.00) 		0.304
(1.00) 		1
(1.00)
RBMS3 6 (3%) 218 0.294
(1.00) 		0.841
(1.00) 		1
(1.00) 		1
(1.00) 		0.406
(1.00)
COL6A6 16 (7%) 208 0.0612
(1.00) 		0.496
(1.00) 		0.00426
(1.00) 		0.381
(1.00) 		0.704
(1.00) 		0.458
(1.00) 		0.736
(1.00)
TMBIM4 4 (2%) 220 1
(1.00) 		1
(1.00) 		0.65
(1.00) 		1
(1.00) 		1
(1.00)
FAM135B 15 (7%) 209 0.0233
(1.00) 		0.0471
(1.00) 		0.116
(1.00) 		0.346
(1.00) 		0.295
(1.00) 		0.107
(1.00) 		0.354
(1.00)
CYP7B1 7 (3%) 217 0.0102
(1.00) 		0.0593
(1.00) 		0.108
(1.00) 		0.0476
(1.00) 		0.00824
(1.00) 		1
(1.00) 		0.351
(1.00)
SLC16A7 9 (4%) 215 0.0291
(1.00) 		0.101
(1.00) 		0.119
(1.00) 		0.777
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.0747
(1.00)
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.17

Table S1.  Gene #1: 'FBXW7 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
FBXW7 MUTATED 4 24 8 2
FBXW7 WILD-TYPE 82 59 28 14

Figure S1.  Get High-res Image Gene #1: 'FBXW7 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1.37e-06 (Fisher's exact test), Q value = 0.0019

Table S2.  Gene #5: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
BRAF MUTATED 13 1 1 5
BRAF WILD-TYPE 31 56 66 32

Figure S2.  Get High-res Image Gene #5: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.88e-07 (Fisher's exact test), Q value = 0.00026

Table S3.  Gene #5: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 108 38
BRAF MUTATED 17 2 1
BRAF WILD-TYPE 42 106 37

Figure S3.  Get High-res Image Gene #5: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.058

Table S4.  Gene #5: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
BRAF MUTATED 1 18 3 0
BRAF WILD-TYPE 85 65 33 16

Figure S4.  Get High-res Image Gene #5: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.28e-11 (Fisher's exact test), Q value = 1e-07

Table S5.  Gene #8: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
TP53 MUTATED 68 22 19 9
TP53 WILD-TYPE 18 61 17 7

Figure S5.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FAT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 6.63e-05 (Fisher's exact test), Q value = 0.092

Table S6.  Gene #13: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
FAT4 MUTATED 6 27 3 2
FAT4 WILD-TYPE 80 56 33 14

Figure S6.  Get High-res Image Gene #13: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CDH2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.86e-05 (Fisher's exact test), Q value = 0.054

Table S7.  Gene #35: 'CDH2 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
CDH2 MUTATED 7 0 1 7
CDH2 WILD-TYPE 37 57 66 30

Figure S7.  Get High-res Image Gene #35: 'CDH2 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'FLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.08e-06 (Fisher's exact test), Q value = 0.0043

Table S8.  Gene #40: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
FLG MUTATED 14 0 6 8
FLG WILD-TYPE 30 57 61 29

Figure S8.  Get High-res Image Gene #40: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'DNAH5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.18

Table S9.  Gene #51: 'DNAH5 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
DNAH5 MUTATED 4 24 4 2
DNAH5 WILD-TYPE 82 59 32 14

Figure S9.  Get High-res Image Gene #51: 'DNAH5 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TMEM132D MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.046

Table S10.  Gene #58: 'TMEM132D MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
TMEM132D MUTATED 11 1 1 3
TMEM132D WILD-TYPE 33 56 66 34

Figure S10.  Get High-res Image Gene #58: 'TMEM132D MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'GRIA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1.09e-07 (Chi-square test), Q value = 0.00015

Table S11.  Gene #89: 'GRIA1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 15 14 4 9 49
GRIA1 MUTATED 0 1 0 2 0 0
GRIA1 WILD-TYPE 29 14 14 2 9 49

Figure S11.  Get High-res Image Gene #89: 'GRIA1 MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'ANK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #100: 'ANK2 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 108 38
ANK2 MUTATED 16 9 0
ANK2 WILD-TYPE 43 99 38

Figure S12.  Get High-res Image Gene #100: 'ANK2 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'ZC3H13 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #109: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 108 38
ZC3H13 MUTATED 14 4 1
ZC3H13 WILD-TYPE 45 104 37

Figure S13.  Get High-res Image Gene #109: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'ZC3H13 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.41e-05 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #109: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
ZC3H13 MUTATED 2 18 1 0
ZC3H13 WILD-TYPE 84 65 35 16

Figure S14.  Get High-res Image Gene #109: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'DOCK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.22

Table S15.  Gene #119: 'DOCK2 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
DOCK2 MUTATED 8 1 1 7
DOCK2 WILD-TYPE 36 56 66 30

Figure S15.  Get High-res Image Gene #119: 'DOCK2 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'DOCK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.19

Table S16.  Gene #119: 'DOCK2 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
DOCK2 MUTATED 1 17 2 1
DOCK2 WILD-TYPE 85 66 34 15

Figure S16.  Get High-res Image Gene #119: 'DOCK2 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CDH10 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.085

Table S17.  Gene #138: 'CDH10 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
CDH10 MUTATED 4 0 1 8
CDH10 WILD-TYPE 40 57 66 29

Figure S17.  Get High-res Image Gene #138: 'CDH10 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CDH10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.18

Table S18.  Gene #138: 'CDH10 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
CDH10 MUTATED 0 13 1 0
CDH10 WILD-TYPE 86 70 35 16

Figure S18.  Get High-res Image Gene #138: 'CDH10 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'SYNE1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.052

Table S19.  Gene #142: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 57 67 37
SYNE1 MUTATED 14 8 6 17
SYNE1 WILD-TYPE 30 49 61 20

Figure S19.  Get High-res Image Gene #142: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'SYNE1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 9.65e-06 (Fisher's exact test), Q value = 0.013

Table S20.  Gene #142: 'SYNE1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 108 38
SYNE1 MUTATED 26 16 3
SYNE1 WILD-TYPE 33 92 35

Figure S20.  Get High-res Image Gene #142: 'SYNE1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'SYNE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.0023

Table S21.  Gene #142: 'SYNE1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 86 83 36 16
SYNE1 MUTATED 7 32 6 0
SYNE1 WILD-TYPE 79 51 30 16

Figure S21.  Get High-res Image Gene #142: 'SYNE1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'ZNF585A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 3.69e-05 (Chi-square test), Q value = 0.051

Table S22.  Gene #184: 'ZNF585A MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 15 14 4 9 49
ZNF585A MUTATED 1 0 0 0 3 0
ZNF585A WILD-TYPE 28 15 14 4 6 49

Figure S22.  Get High-res Image Gene #184: 'ZNF585A MUTATION STATUS' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = COADREAD-TP.mutsig.cluster.txt

  • Molecular subtypes file = COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 224

  • Number of significantly mutated genes = 209

  • Number of Molecular subtypes = 8

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

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

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

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] 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)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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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