Correlation between gene mutation status and molecular subtypes
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.

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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