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 120 genes and 7 molecular subtypes across 155 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • TP53 mutation correlated to 'CN_CNMF'.

  • FAT4 mutation correlated to 'CN_CNMF'.

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

  • DNAH5 mutation correlated to 'MRNA_CNMF'.

  • CASP8 mutation correlated to 'MRNA_CHIERARCHICAL'.

  • ZC3H13 mutation correlated to 'MRNA_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 120 genes and 7 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 12 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
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 Fisher's exact test Fisher's exact test
BRAF 20 (13%) 135 5.58e-06
(0.00427) 		8.43e-08
(6.47e-05) 		8.5e-05
(0.0648) 		0.844
(1.00) 		0.536
(1.00) 		0.145
(1.00) 		1
(1.00)
FLG 26 (17%) 129 0.000232
(0.176) 		0.00927
(1.00) 		0.00027
(0.205) 		0.0772
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.61
(1.00)
SYNE1 37 (24%) 118 0.000146
(0.111) 		0.000472
(0.356) 		0.000289
(0.218) 		0.49
(1.00) 		0.676
(1.00) 		1
(1.00) 		0.181
(1.00)
TP53 75 (48%) 80 0.00371
(1.00) 		0.00883
(1.00) 		1.08e-09
(8.29e-07) 		0.896
(1.00) 		0.862
(1.00) 		0.366
(1.00) 		0.807
(1.00)
FAT4 29 (19%) 126 0.0176
(1.00) 		0.0068
(1.00) 		0.000172
(0.131) 		0.271
(1.00) 		0.743
(1.00) 		0.241
(1.00) 		0.0218
(1.00)
DNAH5 28 (18%) 127 4.26e-06
(0.00326) 		0.00131
(0.974) 		0.0134
(1.00) 		0.31
(1.00) 		0.72
(1.00) 		0.585
(1.00) 		0.642
(1.00)
CASP8 10 (6%) 145 0.000518
(0.39) 		1.21e-05
(0.00921) 		0.00174
(1.00) 		0.726
(1.00) 		1
(1.00) 		1
(1.00) 		0.255
(1.00)
ZC3H13 17 (11%) 138 0.00144
(1.00) 		0.000266
(0.202) 		0.00682
(1.00) 		0.692
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.41
(1.00)
APC 103 (66%) 52 0.0438
(1.00) 		0.0286
(1.00) 		0.101
(1.00) 		0.164
(1.00) 		0.219
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 29 (19%) 126 0.176
(1.00) 		0.109
(1.00) 		0.000825
(0.618) 		0.0419
(1.00) 		0.0719
(1.00) 		0.583
(1.00) 		0.657
(1.00)
KRAS 58 (37%) 97 0.00324
(1.00) 		0.000947
(0.708) 		0.15
(1.00) 		0.613
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.613
(1.00)
NRAS 15 (10%) 140 0.131
(1.00) 		0.408
(1.00) 		0.531
(1.00) 		0.473
(1.00) 		0.536
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 26 (17%) 129 0.252
(1.00) 		0.385
(1.00) 		0.0178
(1.00) 		0.0171
(1.00) 		0.0751
(1.00) 		1
(1.00) 		0.592
(1.00)
SMAD4 18 (12%) 137 0.212
(1.00) 		0.581
(1.00) 		0.01
(1.00) 		0.793
(1.00) 		0.126
(1.00) 		1
(1.00) 		1
(1.00)
FAM123B 19 (12%) 136 0.168
(1.00) 		0.0336
(1.00) 		0.019
(1.00) 		0.363
(1.00) 		0.453
(1.00) 		0.498
(1.00) 		0.498
(1.00)
TTN 69 (45%) 86 0.00599
(1.00) 		0.00803
(1.00) 		0.0011
(0.818) 		0.29
(1.00) 		0.921
(1.00) 		0.655
(1.00) 		0.793
(1.00)
WBSCR17 17 (11%) 138 0.48
(1.00) 		0.376
(1.00) 		0.388
(1.00) 		0.422
(1.00) 		0.357
(1.00) 		0.109
(1.00) 		0.109
(1.00)
ACVR1B 13 (8%) 142 0.27
(1.00) 		0.46
(1.00) 		0.00744
(1.00) 		0.309
(1.00) 		0.0729
(1.00) 		1
(1.00) 		0.386
(1.00)
TNFRSF10C 6 (4%) 149 0.426
(1.00) 		1
(1.00) 		0.0811
(1.00) 		0.133
(1.00) 		0.127
(1.00) 		1
(1.00) 		1
(1.00)
SMAD2 10 (6%) 145 0.028
(1.00) 		0.233
(1.00) 		0.0333
(1.00) 		0.809
(1.00) 		0.565
(1.00) 		0.283
(1.00) 		1
(1.00)
MAP2K4 9 (6%) 146 0.485
(1.00) 		0.133
(1.00) 		0.0512
(1.00) 		0.341
(1.00) 		0.602
(1.00) 		1
(1.00) 		0.255
(1.00)
PCBP1 4 (3%) 151 0.385
(1.00) 		0.386
(1.00) 		0.486
(1.00) 		1
(1.00) 		1
(1.00)
LRP1B 30 (19%) 125 0.00437
(1.00) 		0.00102
(0.765) 		0.00112
(0.836) 		0.549
(1.00) 		0.867
(1.00) 		1
(1.00) 		0.00789
(1.00)
NRXN1 17 (11%) 138 0.21
(1.00) 		0.208
(1.00) 		0.0134
(1.00) 		0.773
(1.00) 		1
(1.00) 		1
(1.00) 		0.455
(1.00)
GRIA1 14 (9%) 141 0.228
(1.00) 		0.103
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.000411
(0.31)
SDK1 25 (16%) 130 0.0158
(1.00) 		0.00187
(1.00) 		0.31
(1.00) 		0.904
(1.00) 		0.638
(1.00) 		1
(1.00) 		0.575
(1.00)
SOX9 9 (6%) 146 0.255
(1.00) 		0.436
(1.00) 		0.585
(1.00) 		0.857
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DMD 27 (17%) 128 0.0222
(1.00) 		0.00627
(1.00) 		0.00855
(1.00) 		0.559
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0998
(1.00)
CNTN6 15 (10%) 140 0.126
(1.00) 		0.162
(1.00) 		0.329
(1.00) 		0.726
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.361
(1.00)
GABRA5 8 (5%) 147 0.663
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.197
(1.00)
OR2M4 8 (5%) 147 0.00569
(1.00) 		0.259
(1.00) 		0.0771
(1.00) 		0.726
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.255
(1.00)
OR6N1 8 (5%) 147 0.00206
(1.00) 		0.00822
(1.00) 		0.00971
(1.00) 		0.226
(1.00) 		1
(1.00)
PCDH9 16 (10%) 139 0.28
(1.00) 		0.711
(1.00) 		0.354
(1.00) 		0.875
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.41
(1.00)
TXNDC3 10 (6%) 145 0.0949
(1.00) 		0.288
(1.00) 		0.0548
(1.00) 		0.453
(1.00) 		0.049
(1.00) 		1
(1.00) 		0.283
(1.00)
MGC26647 7 (5%) 148 0.274
(1.00) 		0.796
(1.00) 		0.887
(1.00) 		0.367
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.166
(1.00)
FAM22F 8 (5%) 147 0.918
(1.00) 		0.272
(1.00) 		0.906
(1.00) 		0.875
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00)
ACVR2A 8 (5%) 147 0.0188
(1.00) 		0.337
(1.00) 		0.098
(1.00) 		0.166
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.255
(1.00)
TCF7L2 11 (7%) 144 0.116
(1.00) 		0.815
(1.00) 		0.0875
(1.00) 		0.624
(1.00) 		1
(1.00) 		1
(1.00) 		0.283
(1.00)
AFF2 15 (10%) 140 0.0104
(1.00) 		0.0293
(1.00) 		0.648
(1.00) 		0.161
(1.00) 		0.111
(1.00) 		0.41
(1.00) 		0.41
(1.00)
CNBD1 6 (4%) 149 0.472
(1.00) 		0.773
(1.00) 		0.312
(1.00) 		1
(1.00) 		0.197
(1.00)
OTOL1 7 (5%) 148 0.385
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.226
(1.00)
KCNA4 10 (6%) 145 0.0778
(1.00) 		0.0895
(1.00) 		0.123
(1.00) 		0.166
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00)
ISL1 8 (5%) 147 0.0987
(1.00) 		0.389
(1.00) 		0.756
(1.00) 		0.445
(1.00) 		1
(1.00) 		1
(1.00) 		0.255
(1.00)
MGC42105 10 (6%) 145 0.00859
(1.00) 		0.103
(1.00) 		0.162
(1.00) 		0.231
(1.00) 		0.111
(1.00) 		1
(1.00) 		1
(1.00)
ACOT4 3 (2%) 152 0.676
(1.00) 		0.396
(1.00) 		0.736
(1.00) 		1
(1.00) 		1
(1.00)
CDH11 13 (8%) 142 0.132
(1.00) 		0.168
(1.00) 		0.258
(1.00) 		1
(1.00) 		1
(1.00) 		0.336
(1.00) 		1
(1.00)
ATM 21 (14%) 134 0.116
(1.00) 		0.435
(1.00) 		0.00208
(1.00) 		0.469
(1.00) 		1
(1.00) 		1
(1.00) 		0.0702
(1.00)
TPTE 11 (7%) 144 0.0132
(1.00) 		0.288
(1.00) 		0.129
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.31
(1.00)
BTNL8 3 (2%) 152 0.343
(1.00) 		0.396
(1.00) 		0.317
(1.00) 		0.166
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KLHL4 12 (8%) 143 0.00859
(1.00) 		0.202
(1.00) 		0.00618
(1.00) 		0.0614
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.283
(1.00)
ROBO1 14 (9%) 141 0.119
(1.00) 		0.0543
(1.00) 		0.0866
(1.00) 		0.0787
(1.00) 		0.796
(1.00) 		1
(1.00) 		0.386
(1.00)
GGT1 3 (2%) 152 0.317
(1.00) 		1
(1.00) 		1
(1.00)
PCDHB2 13 (8%) 142 0.0404
(1.00) 		0.0108
(1.00) 		0.0912
(1.00) 		0.773
(1.00) 		1
(1.00) 		1
(1.00) 		0.336
(1.00)
POSTN 11 (7%) 144 0.27
(1.00) 		0.501
(1.00) 		0.0759
(1.00) 		0.269
(1.00) 		0.406
(1.00) 		1
(1.00) 		1
(1.00)
OR51V1 9 (6%) 146 0.00622
(1.00) 		0.00439
(1.00) 		0.00436
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		0.283
(1.00)
GRIK3 14 (9%) 141 0.33
(1.00) 		0.0396
(1.00) 		0.476
(1.00) 		0.549
(1.00) 		0.536
(1.00) 		1
(1.00) 		1
(1.00)
LRRN3 9 (6%) 146 0.0188
(1.00) 		0.0772
(1.00) 		0.288
(1.00) 		0.166
(1.00) 		0.139
(1.00) 		0.226
(1.00) 		1
(1.00)
PRDM9 11 (7%) 144 0.00152
(1.00) 		0.501
(1.00) 		0.129
(1.00) 		0.127
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.336
(1.00)
ADAM29 9 (6%) 146 0.809
(1.00) 		0.354
(1.00) 		0.268
(1.00) 		1
(1.00) 		1
(1.00)
KIAA1486 9 (6%) 146 0.817
(1.00) 		0.631
(1.00) 		0.469
(1.00) 		0.624
(1.00) 		1
(1.00) 		1
(1.00) 		0.255
(1.00)
PSG8 8 (5%) 147 0.406
(1.00) 		0.511
(1.00) 		0.197
(1.00) 		0.226
(1.00) 		0.102
(1.00)
NCKAP5 13 (8%) 142 0.166
(1.00) 		0.0505
(1.00) 		0.143
(1.00) 		0.0172
(1.00) 		1
(1.00) 		1
(1.00) 		0.361
(1.00)
C8B 9 (6%) 146 0.194
(1.00) 		0.174
(1.00) 		0.853
(1.00) 		0.809
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CCDC160 5 (3%) 150 0.521
(1.00) 		0.831
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.166
(1.00)
DCAF4L2 9 (6%) 146 0.0567
(1.00) 		0.00439
(1.00) 		0.232
(1.00) 		1
(1.00) 		1
(1.00)
DKK2 5 (3%) 150 0.00642
(1.00) 		0.0245
(1.00) 		0.506
(1.00) 		0.445
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00)
EPHA3 13 (8%) 142 0.00394
(1.00) 		0.0543
(1.00) 		0.258
(1.00) 		0.143
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.361
(1.00)
ERBB4 14 (9%) 141 0.112
(1.00) 		0.165
(1.00) 		0.0538
(1.00) 		0.913
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.361
(1.00)
GUCY1A3 10 (6%) 145 0.171
(1.00) 		0.233
(1.00) 		0.227
(1.00) 		1
(1.00) 		0.283
(1.00)
IFT80 7 (5%) 148 0.155
(1.00) 		0.027
(1.00) 		0.135
(1.00) 		0.197
(1.00) 		1
(1.00)
INHBA 7 (5%) 148 0.113
(1.00) 		0.25
(1.00) 		0.312
(1.00) 		0.166
(1.00) 		0.166
(1.00)
KLK2 3 (2%) 152 1
(1.00) 		0.198
(1.00) 		0.736
(1.00) 		1
(1.00)
LPPR4 11 (7%) 144 0.132
(1.00) 		0.0111
(1.00) 		0.283
(1.00) 		0.0908
(1.00) 		0.757
(1.00) 		1
(1.00) 		1
(1.00)
OR7C1 6 (4%) 149 0.0296
(1.00) 		0.0379
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.197
(1.00)
SCN7A 12 (8%) 143 0.00115
(0.858) 		0.0116
(1.00) 		0.161
(1.00) 		0.308
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.336
(1.00)
TGFBR2 7 (5%) 148 0.0293
(1.00) 		0.23
(1.00) 		0.0609
(1.00) 		0.197
(1.00) 		0.197
(1.00)
TRPS1 13 (8%) 142 0.0891
(1.00) 		0.233
(1.00) 		0.000547
(0.411) 		1
(1.00) 		0.336
(1.00)
OR8J1 4 (3%) 151 0.0844
(1.00) 		0.319
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.103
(1.00)
RIMS2 12 (8%) 143 0.00804
(1.00) 		0.282
(1.00) 		0.0429
(1.00) 		0.624
(1.00) 		1
(1.00) 		1
(1.00) 		0.336
(1.00)
SFMBT2 12 (8%) 143 0.45
(1.00) 		0.259
(1.00) 		0.21
(1.00) 		0.857
(1.00) 		1
(1.00) 		1
(1.00) 		0.361
(1.00)
IL18R1 8 (5%) 147 0.286
(1.00) 		0.259
(1.00) 		0.294
(1.00) 		0.624
(1.00) 		1
(1.00) 		1
(1.00) 		0.255
(1.00)
PCDH17 14 (9%) 141 0.347
(1.00) 		0.927
(1.00) 		0.673
(1.00) 		0.624
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.361
(1.00)
FLRT2 11 (7%) 144 0.68
(1.00) 		0.789
(1.00) 		0.367
(1.00) 		0.171
(1.00) 		1
(1.00) 		1
(1.00) 		0.283
(1.00)
PTEN 4 (3%) 151 0.017
(1.00) 		0.688
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.135
(1.00)
ZFHX4 17 (11%) 138 0.516
(1.00) 		0.376
(1.00) 		0.455
(1.00) 		0.875
(1.00) 		1
(1.00) 		1
(1.00) 		0.0452
(1.00)
NRXN3 15 (10%) 140 0.00109
(0.816) 		0.0385
(1.00) 		0.0506
(1.00) 		1
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.386
(1.00)
LIFR 13 (8%) 142 0.0325
(1.00) 		0.578
(1.00) 		0.355
(1.00) 		1
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.0253
(1.00)
ZNF429 7 (5%) 148 0.0908
(1.00) 		0.511
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.197
(1.00)
OR2M2 6 (4%) 149 0.406
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.166
(1.00)
TMEM132D 15 (10%) 140 0.000353
(0.267) 		0.000781
(0.587) 		0.0272
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SAT1 4 (3%) 151 0.00392
(1.00) 		0.071
(1.00) 		0.619
(1.00) 		0.453
(1.00) 		0.0756
(1.00) 		1
(1.00) 		1
(1.00)
CDH18 10 (6%) 145 0.0179
(1.00) 		0.165
(1.00) 		0.0471
(1.00) 		0.285
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.283
(1.00)
P2RY10 6 (4%) 149 0.328
(1.00) 		0.442
(1.00) 		0.744
(1.00) 		1
(1.00) 		1
(1.00)
SYT16 6 (4%) 149 0.0293
(1.00) 		0.101
(1.00) 		0.0596
(1.00) 		0.453
(1.00) 		0.406
(1.00) 		0.197
(1.00) 		1
(1.00)
DKK4 4 (3%) 151 0.071
(1.00) 		0.071
(1.00) 		0.188
(1.00) 		1
(1.00) 		1
(1.00)
NALCN 14 (9%) 141 0.012
(1.00) 		0.092
(1.00) 		0.0129
(1.00) 		0.755
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.361
(1.00)
SULT1C4 3 (2%) 152 0.0124
(1.00) 		0.027
(1.00) 		0.0684
(1.00) 		1
(1.00)
UMOD 7 (5%) 148 0.117
(1.00) 		0.136
(1.00) 		0.166
(1.00) 		0.453
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.135
(1.00)
CPXCR1 6 (4%) 149 0.071
(1.00) 		0.151
(1.00) 		0.574
(1.00) 		0.197
(1.00) 		0.0141
(1.00)
PDZRN4 12 (8%) 143 0.00509
(1.00) 		0.00295
(1.00) 		0.00593
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.31
(1.00)
USP17L2 7 (5%) 148 0.329
(1.00) 		0.337
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.197
(1.00) 		0.197
(1.00)
ESR1 11 (7%) 144 0.135
(1.00) 		0.0736
(1.00) 		0.105
(1.00) 		0.453
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.283
(1.00)
FAM5C 10 (6%) 145 0.118
(1.00) 		0.389
(1.00) 		0.0471
(1.00) 		0.269
(1.00) 		0.565
(1.00) 		0.283
(1.00) 		0.283
(1.00)
MIER3 10 (6%) 145 0.000875
(0.656) 		0.00803
(1.00) 		0.00303
(1.00) 		0.773
(1.00) 		1
(1.00) 		1
(1.00) 		0.31
(1.00)
NLRP5 10 (6%) 145 0.0259
(1.00) 		0.732
(1.00) 		0.162
(1.00) 		1
(1.00) 		0.255
(1.00)
OR6T1 6 (4%) 149 0.934
(1.00) 		0.59
(1.00) 		0.744
(1.00) 		0.166
(1.00) 		1
(1.00)
PCDH10 14 (9%) 141 0.136
(1.00) 		0.162
(1.00) 		0.237
(1.00) 		0.467
(1.00) 		1
(1.00) 		1
(1.00) 		0.361
(1.00)
PCDHB5 12 (8%) 143 0.087
(1.00) 		0.282
(1.00) 		0.161
(1.00) 		0.549
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.31
(1.00)
TRPC6 8 (5%) 147 0.105
(1.00) 		0.796
(1.00) 		0.35
(1.00) 		1
(1.00) 		0.197
(1.00)
RHOA 4 (3%) 151 0.619
(1.00) 		0.135
(1.00) 		1
(1.00)
CYTL1 4 (3%) 151 0.287
(1.00) 		0.776
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.135
(1.00)
CHRM2 8 (5%) 147 0.472
(1.00) 		0.25
(1.00) 		0.138
(1.00) 		0.857
(1.00) 		1
(1.00) 		0.226
(1.00) 		0.226
(1.00)
GALNT14 9 (6%) 146 0.177
(1.00) 		0.541
(1.00) 		0.0807
(1.00) 		0.0332
(1.00) 		0.0642
(1.00) 		1
(1.00) 		0.226
(1.00)
LRRIQ3 7 (5%) 148 0.635
(1.00) 		0.433
(1.00) 		0.47
(1.00) 		0.166
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.226
(1.00)
NAALAD2 11 (7%) 144 0.0262
(1.00) 		0.0381
(1.00) 		0.0127
(1.00) 		0.624
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.283
(1.00)
PCDH11X 11 (7%) 144 0.102
(1.00) 		0.501
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.31
(1.00)
TFAP2D 5 (3%) 150 0.582
(1.00) 		0.864
(1.00) 		0.506
(1.00) 		0.726
(1.00) 		0.511
(1.00) 		1
(1.00) 		1
(1.00)
TNR 15 (10%) 140 0.0139
(1.00) 		0.0253
(1.00) 		0.00125
(0.931) 		0.341
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CNTNAP4 10 (6%) 145 0.0102
(1.00) 		0.688
(1.00) 		0.0226
(1.00) 		0.346
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.0325
(1.00)
DOCK2 16 (10%) 139 0.00245
(1.00) 		0.00388
(1.00) 		0.00754
(1.00) 		0.334
(1.00) 		0.536
(1.00) 		1
(1.00) 		0.433
(1.00)
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 5.58e-06 (Fisher's exact test), Q value = 0.0043

Table S1.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 58 29 24
BRAF MUTATED 12 1 4 1
BRAF WILD-TYPE 18 57 25 23

Figure S1.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 8.43e-08 (Fisher's exact test), Q value = 6.5e-05

Table S2.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 43 45
BRAF MUTATED 1 16 1
BRAF WILD-TYPE 52 27 44

Figure S2.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 8.5e-05 (Fisher's exact test), Q value = 0.065

Table S3.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 64 11 8
BRAF MUTATED 2 18 0 0
BRAF WILD-TYPE 68 46 11 8

Figure S3.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 8.3e-07

Table S4.  Gene #7: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 64 11 8
TP53 MUTATED 51 13 4 6
TP53 WILD-TYPE 19 51 7 2

Figure S4.  Get High-res Image Gene #7: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FAT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.13

Table S5.  Gene #17: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 64 11 8
FAT4 MUTATED 4 22 1 1
FAT4 WILD-TYPE 66 42 10 7

Figure S5.  Get High-res Image Gene #17: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 58 29 24
FLG MUTATED 10 2 8 2
FLG WILD-TYPE 20 56 21 22

Figure S6.  Get High-res Image Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'FLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.2

Table S7.  Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 64 11 8
FLG MUTATED 3 18 1 3
FLG WILD-TYPE 67 46 10 5

Figure S7.  Get High-res Image Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'DNAH5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.26e-06 (Fisher's exact test), Q value = 0.0033

Table S8.  Gene #60: 'DNAH5 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 58 29 24
DNAH5 MUTATED 13 4 9 0
DNAH5 WILD-TYPE 17 54 20 24

Figure S8.  Get High-res Image Gene #60: 'DNAH5 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0092

Table S9.  Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 43 45
CASP8 MUTATED 0 9 0
CASP8 WILD-TYPE 53 34 45

Figure S9.  Get High-res Image Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'ZC3H13 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000266 (Fisher's exact test), Q value = 0.2

Table S10.  Gene #82: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 43 45
ZC3H13 MUTATED 3 12 1
ZC3H13 WILD-TYPE 50 31 44

Figure S10.  Get High-res Image Gene #82: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'SYNE1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.11

Table S11.  Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 58 29 24
SYNE1 MUTATED 13 7 14 3
SYNE1 WILD-TYPE 17 51 15 21

Figure S11.  Get High-res Image Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'SYNE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.22

Table S12.  Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 64 11 8
SYNE1 MUTATED 9 26 0 1
SYNE1 WILD-TYPE 61 38 11 7

Figure S12.  Get High-res Image Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 155

  • Number of significantly mutated genes = 120

  • Number of Molecular subtypes = 7

  • 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

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] 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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