Correlation between gene mutation status and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1XS5S9T
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5S9T
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
(0.00454) 		8.43e-08
(6.87e-05) 		8.5e-05
(0.0689) 		0.734
(1.00) 		0.926
(1.00) 		0.145
(1.00) 		1
(1.00)
FLG 26 (17%) 129 0.000232
(0.188) 		0.00927
(1.00) 		0.00027
(0.218) 		0.232
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.61
(1.00)
SYNE1 37 (24%) 118 0.000146
(0.118) 		0.000472
(0.379) 		0.000289
(0.232) 		0.729
(1.00) 		0.78
(1.00) 		1
(1.00) 		0.181
(1.00)
TP53 75 (48%) 80 0.00371
(1.00) 		0.00883
(1.00) 		1.08e-09
(8.81e-07) 		0.403
(1.00) 		0.38
(1.00) 		0.366
(1.00) 		0.807
(1.00)
FAT4 29 (19%) 126 0.0176
(1.00) 		0.0068
(1.00) 		0.000172
(0.14) 		0.419
(1.00) 		0.322
(1.00) 		0.241
(1.00) 		0.0218
(1.00)
DNAH5 28 (18%) 127 4.26e-06
(0.00347) 		0.00131
(1.00) 		0.0134
(1.00) 		0.693
(1.00) 		0.12
(1.00) 		0.585
(1.00) 		0.642
(1.00)
CASP8 10 (6%) 145 0.000518
(0.415) 		1.21e-05
(0.00979) 		0.00174
(1.00) 		0.0587
(1.00) 		0.208
(1.00) 		1
(1.00) 		0.255
(1.00)
ZC3H13 17 (11%) 138 0.00144
(1.00) 		0.000266
(0.215) 		0.00682
(1.00) 		0.281
(1.00) 		0.0214
(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) 		0.7
(1.00) 		0.388
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 29 (19%) 126 0.176
(1.00) 		0.109
(1.00) 		0.000825
(0.658) 		0.00533
(1.00) 		0.233
(1.00) 		0.583
(1.00) 		0.657
(1.00)
KRAS 58 (37%) 97 0.00324
(1.00) 		0.000947
(0.754) 		0.15
(1.00) 		0.772
(1.00) 		0.752
(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) 		0.0659
(1.00) 		0.332
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 26 (17%) 129 0.252
(1.00) 		0.385
(1.00) 		0.0178
(1.00) 		0.218
(1.00) 		0.332
(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) 		0.4
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00)
FAM123B 19 (12%) 136 0.168
(1.00) 		0.0336
(1.00) 		0.019
(1.00) 		0.579
(1.00) 		0.422
(1.00) 		0.498
(1.00) 		0.498
(1.00)
TTN 69 (45%) 86 0.00599
(1.00) 		0.00803
(1.00) 		0.0011
(0.87) 		0.421
(1.00) 		0.653
(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) 		0.877
(1.00) 		0.305
(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) 		0.579
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.386
(1.00)
TNFRSF10C 6 (4%) 149 0.426
(1.00) 		1
(1.00) 		0.0811
(1.00) 		0.618
(1.00) 		0.169
(1.00) 		1
(1.00) 		1
(1.00)
SMAD2 10 (6%) 145 0.028
(1.00) 		0.233
(1.00) 		0.0333
(1.00) 		0.943
(1.00) 		0.377
(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) 		0.446
(1.00) 		0.536
(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
(0.814) 		0.00112
(0.89) 		0.0856
(1.00) 		0.0928
(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) 		0.375
(1.00) 		0.771
(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) 		0.0589
(1.00) 		0.47
(1.00) 		1
(1.00) 		0.000411
(0.33)
SDK1 25 (16%) 130 0.0158
(1.00) 		0.00187
(1.00) 		0.31
(1.00) 		0.125
(1.00) 		0.529
(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) 		0.14
(1.00) 		0.461
(1.00) 		1
(1.00) 		1
(1.00)
DMD 27 (17%) 128 0.0222
(1.00) 		0.00627
(1.00) 		0.00855
(1.00) 		0.357
(1.00) 		0.0815
(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) 		0.833
(1.00) 		0.25
(1.00) 		1
(1.00) 		0.361
(1.00)
GABRA5 8 (5%) 147 0.663
(1.00) 		1
(1.00) 		1
(1.00) 		0.0749
(1.00) 		0.592
(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) 		0.767
(1.00) 		0.817
(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) 		0.618
(1.00) 		1
(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) 		0.847
(1.00) 		0.47
(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) 		0.523
(1.00) 		0.0878
(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) 		1
(1.00) 		0.201
(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) 		0.345
(1.00) 		0.445
(1.00) 		1
(1.00) 		1
(1.00)
ACVR2A 8 (5%) 147 0.0188
(1.00) 		0.337
(1.00) 		0.098
(1.00) 		0.167
(1.00) 		0.668
(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) 		0.947
(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) 		0.5
(1.00) 		0.123
(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) 		0.159
(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) 		0.0221
(1.00) 		0.039
(1.00) 		1
(1.00) 		1
(1.00)
ISL1 8 (5%) 147 0.0987
(1.00) 		0.389
(1.00) 		0.756
(1.00) 		0.767
(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) 		0.266
(1.00) 		0.297
(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) 		0.699
(1.00) 		0.266
(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) 		0.306
(1.00) 		0.697
(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) 		0.212
(1.00) 		0.668
(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) 		0.531
(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) 		0.344
(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) 		0.205
(1.00) 		0.356
(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) 		0.388
(1.00) 		0.786
(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) 		0.618
(1.00) 		0.346
(1.00) 		1
(1.00) 		1
(1.00)
OR51V1 9 (6%) 146 0.00622
(1.00) 		0.00439
(1.00) 		0.00436
(1.00) 		1
(1.00) 		0.745
(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) 		0.464
(1.00) 		0.331
(1.00) 		1
(1.00) 		1
(1.00)
LRRN3 9 (6%) 146 0.0188
(1.00) 		0.0772
(1.00) 		0.288
(1.00) 		0.196
(1.00) 		0.208
(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) 		0.339
(1.00) 		1
(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) 		0.531
(1.00) 		0.143
(1.00) 		1
(1.00) 		1
(1.00)
KIAA1486 9 (6%) 146 0.817
(1.00) 		0.631
(1.00) 		0.469
(1.00) 		0.405
(1.00) 		0.733
(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) 		0.461
(1.00) 		0.501
(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) 		0.0165
(1.00) 		0.731
(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) 		0.73
(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) 		0.461
(1.00) 		1
(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) 		0.618
(1.00) 		0.346
(1.00) 		1
(1.00) 		1
(1.00)
DKK2 5 (3%) 150 0.00642
(1.00) 		0.0245
(1.00) 		0.506
(1.00) 		0.108
(1.00) 		0.592
(1.00) 		1
(1.00) 		1
(1.00)
EPHA3 13 (8%) 142 0.00394
(1.00) 		0.0543
(1.00) 		0.258
(1.00) 		0.388
(1.00) 		0.786
(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) 		0.198
(1.00) 		0.0738
(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) 		0.668
(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) 		0.523
(1.00) 		0.501
(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) 		0.919
(1.00) 		0.346
(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) 		0.0521
(1.00) 		0.297
(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
(0.913) 		0.0116
(1.00) 		0.161
(1.00) 		0.339
(1.00) 		0.905
(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) 		0.515
(1.00) 		0.27
(1.00) 		0.197
(1.00) 		0.197
(1.00)
TRPS1 13 (8%) 142 0.0891
(1.00) 		0.233
(1.00) 		0.000547
(0.438) 		1
(1.00) 		0.821
(1.00) 		1
(1.00) 		0.336
(1.00)
OR8J1 4 (3%) 151 0.0844
(1.00) 		0.319
(1.00) 		0.619
(1.00) 		0.851
(1.00) 		1
(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) 		0.167
(1.00) 		0.668
(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) 		0.0986
(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) 		0.767
(1.00) 		0.817
(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) 		0.631
(1.00) 		0.329
(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) 		0.592
(1.00) 		0.786
(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) 		0.517
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.0452
(1.00)
NRXN3 15 (10%) 140 0.00109
(0.869) 		0.0385
(1.00) 		0.0506
(1.00) 		0.631
(1.00) 		0.25
(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) 		0.723
(1.00) 		0.445
(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) 		0.618
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.197
(1.00)
OR2M2 6 (4%) 149 0.406
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.442
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.166
(1.00)
TMEM132D 15 (10%) 140 0.000353
(0.284) 		0.000781
(0.624) 		0.0272
(1.00) 		0.101
(1.00) 		0.329
(1.00) 		1
(1.00) 		1
(1.00)
SAT1 4 (3%) 151 0.00392
(1.00) 		0.071
(1.00) 		0.619
(1.00) 		0.531
(1.00) 		0.143
(1.00) 		1
(1.00) 		1
(1.00)
CDH18 10 (6%) 145 0.0179
(1.00) 		0.165
(1.00) 		0.0471
(1.00) 		0.122
(1.00) 		0.298
(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) 		0.523
(1.00) 		0.501
(1.00) 		1
(1.00) 		1
(1.00)
SYT16 6 (4%) 149 0.0293
(1.00) 		0.101
(1.00) 		0.0596
(1.00) 		0.314
(1.00) 		0.673
(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) 		0.176
(1.00) 		0.397
(1.00) 		1
(1.00) 		1
(1.00)
NALCN 14 (9%) 141 0.012
(1.00) 		0.092
(1.00) 		0.0129
(1.00) 		0.474
(1.00) 		0.771
(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) 		0.347
(1.00) 		0.0961
(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) 		0.478
(1.00) 		1
(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) 		0.0425
(1.00) 		0.168
(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) 		0.135
(1.00) 		0.318
(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) 		0.515
(1.00) 		0.0961
(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) 		0.284
(1.00) 		0.297
(1.00) 		0.283
(1.00) 		0.283
(1.00)
MIER3 10 (6%) 145 0.000875
(0.698) 		0.00803
(1.00) 		0.00303
(1.00) 		0.569
(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) 		0.405
(1.00) 		0.231
(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) 		0.737
(1.00) 		1
(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) 		0.579
(1.00) 		0.541
(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) 		0.177
(1.00) 		0.0126
(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) 		0.618
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.197
(1.00)
RHOA 4 (3%) 151 0.619
(1.00) 		1
(1.00) 		1
(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) 		0.405
(1.00) 		0.733
(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) 		0.685
(1.00) 		0.0586
(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) 		0.523
(1.00) 		0.364
(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) 		0.0972
(1.00) 		0.0154
(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) 		0.108
(1.00) 		0.217
(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) 		0.804
(1.00) 		0.673
(1.00) 		1
(1.00) 		1
(1.00)
TNR 15 (10%) 140 0.0139
(1.00) 		0.0253
(1.00) 		0.00125
(0.991) 		0.197
(1.00) 		0.298
(1.00) 		1
(1.00) 		1
(1.00)
CNTNAP4 10 (6%) 145 0.0102
(1.00) 		0.688
(1.00) 		0.0226
(1.00) 		0.425
(1.00) 		0.733
(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) 		0.889
(1.00) 		0.412
(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 = 0.0045

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 = 6.9e-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 = 0.069

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 = 8.8e-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 = 0.14

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 = 0.19

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 = 0.22

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 = 0.0035

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 = 0.0098

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 = 0.21

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 = 0.12

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 = 0.23

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.

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] 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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