Correlation between gene mutation status and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.

Summary

Testing the association between mutation status of 120 genes and 10 clinical features across 155 patients, 23 significant findings detected with Q value < 0.25.

  • BRAF mutation correlated to 'HISTOLOGICAL.TYPE'.

  • NRXN1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • ACVR2A mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • CNBD1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • BTNL8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • GGT1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • GRIK3 mutation correlated to 'AGE'.

  • CASP8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • ERBB4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • IFT80 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • OR8J1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • ZFHX4 mutation correlated to 'Time to Death'.

  • ZNF429 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • DKK4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • NALCN mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • SULT1C4 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • UMOD mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • USP17L2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • FAM5C mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • OR6T1 mutation correlated to 'AGE'.

  • CYTL1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • NAALAD2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

  • TNR mutation correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 120 genes and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nMutated (%) nWild-Type logrank test t-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 Fisher's exact test t-test
BRAF 20 (13%) 135 0.82
(1.00) 		0.0257
(1.00) 		0.0586
(1.00) 		1.07e-05
(0.0126) 		0.149
(1.00) 		0.755
(1.00) 		0.401
(1.00) 		0.536
(1.00) 		0.59
(1.00) 		0.822
(1.00)
NRXN1 17 (11%) 138 0.734
(1.00) 		0.592
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.059
(1.00) 		0.0423
(1.00) 		0.732
(1.00) 		0.0599
(1.00) 		0.757
(1.00) 		5.76e-05
(0.0672)
ACVR2A 8 (5%) 147 0.242
(1.00) 		0.703
(1.00) 		0.0337
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.55
(1.00) 		1
(1.00) 		1.69e-06
(0.00198)
CNBD1 6 (4%) 149 0.582
(1.00) 		0.736
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.16
(1.00) 		0.612
(1.00) 		0.13
(1.00) 		1
(1.00) 		5.86e-09
(6.94e-06)
BTNL8 3 (2%) 152 0.0121
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.561
(1.00) 		1
(1.00) 		6.1e-09
(7.2e-06)
GGT1 3 (2%) 152 0.865
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.561
(1.00) 		1
(1.00) 		6.1e-09
(7.2e-06)
GRIK3 14 (9%) 141 0.536
(1.00) 		3.04e-05
(0.0356) 		0.402
(1.00) 		0.465
(1.00) 		0.876
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.707
(1.00) 		0.00185
(1.00)
CASP8 10 (6%) 145 0.417
(1.00) 		0.0469
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.147
(1.00) 		0.125
(1.00) 		0.401
(1.00) 		0.156
(1.00) 		0.444
(1.00) 		2.26e-06
(0.00266)
ERBB4 14 (9%) 141 0.0025
(1.00) 		0.989
(1.00) 		0.101
(1.00) 		0.433
(1.00) 		0.0143
(1.00) 		0.0514
(1.00) 		0.283
(1.00) 		0.108
(1.00) 		0.463
(1.00) 		6.48e-06
(0.00759)
IFT80 7 (5%) 148 0.911
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.867
(1.00) 		0.321
(1.00) 		0.613
(1.00) 		0.552
(1.00) 		1
(1.00) 		3.01e-07
(0.000355)
OR8J1 4 (3%) 151 0.355
(1.00) 		0.273
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.356
(1.00) 		1
(1.00) 		6.02e-09
(7.12e-06)
ZFHX4 17 (11%) 138 2.48e-05
(0.029) 		0.778
(1.00) 		0.453
(1.00) 		0.284
(1.00) 		0.0148
(1.00) 		0.4
(1.00) 		0.725
(1.00) 		0.452
(1.00) 		0.752
(1.00) 		0.038
(1.00)
ZNF429 7 (5%) 148 0.623
(1.00) 		0.22
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.0625
(1.00) 		0.321
(1.00) 		0.612
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.00011
(0.128)
DKK4 4 (3%) 151 0.0582
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.312
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.401
(1.00) 		1
(1.00) 		6.02e-09
(7.12e-06)
NALCN 14 (9%) 141 0.302
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.693
(1.00) 		0.774
(1.00) 		0.147
(1.00) 		0.281
(1.00) 		0.00959
(1.00) 		1
(1.00) 		6.79e-05
(0.0792)
SULT1C4 3 (2%) 152 0.03
(1.00) 		0.931
(1.00) 		1
(1.00) 		0.0651
(1.00) 		0.199
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.561
(1.00) 		1
(1.00) 		6.1e-09
(7.2e-06)
UMOD 7 (5%) 148 0.493
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.313
(1.00) 		0.321
(1.00) 		0.613
(1.00) 		0.412
(1.00) 		0.633
(1.00) 		0.00011
(0.128)
USP17L2 7 (5%) 148 0.302
(1.00) 		0.805
(1.00) 		1
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.0961
(1.00) 		0.613
(1.00) 		0.125
(1.00) 		0.633
(1.00) 		5.78e-09
(6.85e-06)
FAM5C 10 (6%) 145 0.0122
(1.00) 		0.845
(1.00) 		0.21
(1.00) 		0.195
(1.00) 		0.147
(1.00) 		0.125
(1.00) 		0.4
(1.00) 		0.127
(1.00) 		0.639
(1.00) 		5.21e-08
(6.13e-05)
OR6T1 6 (4%) 149 0.502
(1.00) 		0.000122
(0.142) 		0.681
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.624
(1.00) 		0.548
(1.00) 		0.148
(1.00) 		0.535
(1.00) 		0.646
(1.00)
CYTL1 4 (3%) 151 0.248
(1.00) 		1
(1.00) 		1
(1.00) 		0.0483
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.401
(1.00) 		1
(1.00) 		6.02e-09
(7.12e-06)
NAALAD2 11 (7%) 144 0.884
(1.00) 		0.544
(1.00) 		0.13
(1.00) 		0.0156
(1.00) 		0.00551
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.286
(1.00) 		1
(1.00) 		3.34e-05
(0.039)
TNR 15 (10%) 140 0.444
(1.00) 		0.493
(1.00) 		0.588
(1.00) 		0.465
(1.00) 		0.163
(1.00) 		0.00835
(1.00) 		0.722
(1.00) 		0.0146
(1.00) 		1
(1.00) 		1.39e-06
(0.00163)
APC 103 (66%) 52 0.291
(1.00) 		0.627
(1.00) 		0.042
(1.00) 		0.645
(1.00) 		0.797
(1.00) 		0.944
(1.00) 		0.165
(1.00) 		0.272
(1.00) 		0.0378
(1.00) 		0.561
(1.00)
FBXW7 29 (19%) 126 0.841
(1.00) 		0.0362
(1.00) 		0.154
(1.00) 		0.00324
(1.00) 		0.112
(1.00) 		0.604
(1.00) 		0.0169
(1.00) 		0.00243
(1.00) 		0.0795
(1.00) 		0.774
(1.00)
KRAS 58 (37%) 97 0.226
(1.00) 		0.00304
(1.00) 		0.246
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.317
(1.00) 		0.606
(1.00) 		0.315
(1.00) 		0.4
(1.00)
NRAS 15 (10%) 140 0.281
(1.00) 		0.168
(1.00) 		0.0269
(1.00) 		1
(1.00) 		0.489
(1.00) 		0.083
(1.00) 		0.469
(1.00) 		0.732
(1.00) 		0.276
(1.00) 		0.134
(1.00)
PIK3CA 26 (17%) 129 0.661
(1.00) 		0.198
(1.00) 		0.83
(1.00) 		0.134
(1.00) 		0.554
(1.00) 		0.0107
(1.00) 		0.333
(1.00) 		0.028
(1.00) 		0.445
(1.00) 		0.000236
(0.274)
TP53 75 (48%) 80 0.696
(1.00) 		0.0728
(1.00) 		0.336
(1.00) 		0.00383
(1.00) 		0.557
(1.00) 		0.254
(1.00) 		0.558
(1.00) 		0.102
(1.00) 		0.803
(1.00) 		0.122
(1.00)
SMAD4 18 (12%) 137 0.587
(1.00) 		0.833
(1.00) 		0.625
(1.00) 		0.149
(1.00) 		0.949
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.772
(1.00) 		0.414
(1.00)
FAM123B 19 (12%) 136 0.717
(1.00) 		0.527
(1.00) 		0.811
(1.00) 		0.489
(1.00) 		0.675
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.655
(1.00)
TTN 69 (45%) 86 0.625
(1.00) 		0.267
(1.00) 		0.421
(1.00) 		0.0237
(1.00) 		0.281
(1.00) 		0.166
(1.00) 		0.288
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.966
(1.00)
WBSCR17 17 (11%) 138 0.39
(1.00) 		0.0641
(1.00) 		0.803
(1.00) 		1
(1.00) 		0.777
(1.00) 		0.938
(1.00) 		0.732
(1.00) 		0.0503
(1.00) 		0.212
(1.00) 		0.321
(1.00)
ACVR1B 13 (8%) 142 0.759
(1.00) 		0.75
(1.00) 		0.78
(1.00) 		0.0345
(1.00) 		0.0242
(1.00) 		1
(1.00) 		0.721
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.512
(1.00)
TNFRSF10C 6 (4%) 149 0.978
(1.00) 		0.681
(1.00) 		0.59
(1.00) 		0.0968
(1.00) 		0.244
(1.00) 		0.0736
(1.00) 		0.0117
(1.00) 		0.105
(1.00) 		0.178
(1.00)
SMAD2 10 (6%) 145 0.617
(1.00) 		0.805
(1.00) 		0.327
(1.00) 		0.195
(1.00) 		0.401
(1.00) 		0.744
(1.00) 		0.636
(1.00) 		0.453
(1.00) 		0.404
(1.00) 		0.281
(1.00)
MAP2K4 9 (6%) 146 0.0181
(1.00) 		0.243
(1.00) 		0.746
(1.00) 		0.613
(1.00) 		0.504
(1.00) 		0.637
(1.00) 		0.4
(1.00) 		0.382
(1.00) 		0.639
(1.00) 		0.187
(1.00)
PCBP1 4 (3%) 151 0.00453
(1.00) 		1
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.641
(1.00) 		0.0347
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.135
(1.00)
FAT4 29 (19%) 126 0.529
(1.00) 		0.0955
(1.00) 		0.543
(1.00) 		0.155
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.111
(1.00) 		0.118
(1.00) 		0.409
(1.00)
LRP1B 30 (19%) 125 0.805
(1.00) 		0.144
(1.00) 		0.228
(1.00) 		0.00324
(1.00) 		0.662
(1.00) 		0.407
(1.00) 		0.809
(1.00) 		0.406
(1.00) 		0.683
(1.00) 		0.185
(1.00)
GRIA1 14 (9%) 141 0.435
(1.00) 		0.84
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.929
(1.00) 		0.0757
(1.00) 		0.552
(1.00) 		0.728
(1.00) 		0.313
(1.00)
SDK1 25 (16%) 130 0.6
(1.00) 		0.248
(1.00) 		0.52
(1.00) 		0.0663
(1.00) 		0.781
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.497
(1.00) 		0.718
(1.00)
SOX9 9 (6%) 146 0.28
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.255
(1.00) 		1
(1.00) 		0.334
(1.00)
DMD 27 (17%) 128 0.763
(1.00) 		0.517
(1.00) 		0.143
(1.00) 		0.0159
(1.00) 		0.127
(1.00) 		0.616
(1.00) 		0.0297
(1.00) 		0.00022
(0.255) 		0.139
(1.00) 		0.133
(1.00)
CNTN6 15 (10%) 140 0.493
(1.00) 		0.223
(1.00) 		0.0619
(1.00) 		0.708
(1.00) 		0.171
(1.00) 		0.21
(1.00) 		0.217
(1.00) 		0.216
(1.00) 		0.0482
(1.00) 		0.000761
(0.882)
GABRA5 8 (5%) 147 0.165
(1.00) 		0.518
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.915
(1.00) 		1
(1.00) 		0.236
(1.00)
OR2M4 8 (5%) 147 0.587
(1.00) 		0.592
(1.00) 		0.495
(1.00) 		0.357
(1.00) 		0.884
(1.00) 		1
(1.00) 		1
(1.00) 		0.915
(1.00) 		0.639
(1.00) 		0.609
(1.00)
OR6N1 8 (5%) 147 0.914
(1.00) 		0.986
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.886
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.663
(1.00)
PCDH9 16 (10%) 139 0.222
(1.00) 		0.678
(1.00) 		0.429
(1.00) 		0.72
(1.00) 		0.73
(1.00) 		0.764
(1.00) 		0.725
(1.00) 		0.0456
(1.00) 		1
(1.00) 		0.0201
(1.00)
TXNDC3 10 (6%) 145 0.33
(1.00) 		0.517
(1.00) 		0.534
(1.00) 		0.659
(1.00) 		1
(1.00) 		0.901
(1.00) 		0.401
(1.00) 		0.697
(1.00) 		0.651
(1.00) 		0.342
(1.00)
MGC26647 7 (5%) 148 0.863
(1.00) 		0.883
(1.00) 		0.276
(1.00) 		0.305
(1.00) 		0.216
(1.00) 		0.495
(1.00) 		0.613
(1.00) 		0.552
(1.00) 		0.633
(1.00) 		0.0798
(1.00)
FAM22F 8 (5%) 147 0.0582
(1.00) 		0.633
(1.00) 		0.00647
(1.00) 		1
(1.00) 		0.0187
(1.00) 		0.687
(1.00) 		0.1
(1.00) 		0.0887
(1.00) 		0.133
(1.00) 		0.523
(1.00)
TCF7L2 11 (7%) 144 0.347
(1.00) 		0.343
(1.00) 		0.368
(1.00) 		0.214
(1.00) 		0.446
(1.00) 		1
(1.00) 		1
(1.00) 		0.884
(1.00) 		1
(1.00) 		0.319
(1.00)
AFF2 15 (10%) 140 0.808
(1.00) 		0.291
(1.00) 		0.588
(1.00) 		0.0639
(1.00) 		0.476
(1.00) 		0.752
(1.00) 		0.217
(1.00) 		0.115
(1.00) 		0.35
(1.00) 		0.127
(1.00)
OTOL1 7 (5%) 148 0.353
(1.00) 		0.17
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.0625
(1.00) 		0.267
(1.00) 		0.613
(1.00) 		0.507
(1.00) 		0.633
(1.00) 		0.313
(1.00)
KCNA4 10 (6%) 145 0.944
(1.00) 		0.155
(1.00) 		0.534
(1.00) 		0.0525
(1.00) 		0.823
(1.00) 		0.744
(1.00) 		0.401
(1.00) 		0.403
(1.00) 		0.651
(1.00) 		0.527
(1.00)
ISL1 8 (5%) 147 0.548
(1.00) 		0.975
(1.00) 		0.719
(1.00) 		0.357
(1.00) 		0.884
(1.00) 		0.1
(1.00) 		1
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.77
(1.00)
MGC42105 10 (6%) 145 0.597
(1.00) 		0.975
(1.00) 		0.534
(1.00) 		0.659
(1.00) 		0.251
(1.00) 		0.477
(1.00) 		0.621
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.05
(1.00)
ACOT4 3 (2%) 152 0.0294
(1.00) 		1
(1.00) 		0.405
(1.00) 		0.0332
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.477
(1.00) 		0.366
(1.00) 		0.647
(1.00)
CDH11 13 (8%) 142 0.545
(1.00) 		0.982
(1.00) 		0.564
(1.00) 		1
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.7
(1.00) 		0.635
(1.00) 		0.707
(1.00) 		0.362
(1.00)
ATM 21 (14%) 134 0.749
(1.00) 		0.891
(1.00) 		0.106
(1.00) 		0.331
(1.00) 		0.781
(1.00) 		0.421
(1.00) 		0.401
(1.00) 		0.183
(1.00) 		0.59
(1.00) 		0.181
(1.00)
TPTE 11 (7%) 144 0.623
(1.00) 		0.785
(1.00) 		0.368
(1.00) 		0.0736
(1.00) 		0.649
(1.00) 		0.419
(1.00) 		1
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.63
(1.00)
KLHL4 12 (8%) 143 0.2
(1.00) 		0.12
(1.00) 		0.246
(1.00) 		0.0985
(1.00) 		0.0738
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.0836
(1.00) 		0.067
(1.00) 		0.867
(1.00)
ROBO1 14 (9%) 141 0.67
(1.00) 		0.388
(1.00) 		0.78
(1.00) 		0.00676
(1.00) 		0.208
(1.00) 		0.737
(1.00) 		0.722
(1.00) 		0.0418
(1.00) 		1
(1.00) 		0.0402
(1.00)
FLG 26 (17%) 129 0.242
(1.00) 		0.605
(1.00) 		0.673
(1.00) 		0.0274
(1.00) 		0.136
(1.00) 		0.123
(1.00) 		0.326
(1.00) 		0.196
(1.00) 		0.135
(1.00) 		0.0739
(1.00)
PCDHB2 13 (8%) 142 0.307
(1.00) 		0.847
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.568
(1.00) 		0.7
(1.00) 		0.847
(1.00) 		1
(1.00) 		0.457
(1.00)
POSTN 11 (7%) 144 0.0656
(1.00) 		0.929
(1.00) 		1
(1.00) 		0.0736
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.401
(1.00) 		0.248
(1.00) 		0.651
(1.00) 		0.377
(1.00)
OR51V1 9 (6%) 146 0.392
(1.00) 		0.849
(1.00) 		0.327
(1.00) 		0.00536
(1.00) 		0.0471
(1.00) 		0.224
(1.00) 		0.4
(1.00) 		0.0203
(1.00) 		0.651
(1.00) 		0.252
(1.00)
LRRN3 9 (6%) 146 0.997
(1.00) 		0.573
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.25
(1.00) 		0.0802
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.268
(1.00)
PRDM9 11 (7%) 144 0.413
(1.00) 		0.645
(1.00) 		0.368
(1.00) 		0.659
(1.00) 		0.183
(1.00) 		0.625
(1.00) 		0.0339
(1.00) 		0.445
(1.00) 		0.451
(1.00) 		0.399
(1.00)
ADAM29 9 (6%) 146 0.222
(1.00) 		0.651
(1.00) 		0.098
(1.00) 		1
(1.00) 		0.0452
(1.00) 		0.281
(1.00) 		0.0656
(1.00) 		0.0361
(1.00) 		1
(1.00) 		0.000673
(0.781)
KIAA1486 9 (6%) 146 0.137
(1.00) 		0.8
(1.00) 		0.746
(1.00) 		0.152
(1.00) 		0.169
(1.00) 		0.563
(1.00) 		0.4
(1.00) 		0.155
(1.00) 		0.072
(1.00) 		0.555
(1.00)
PSG8 8 (5%) 147 0.287
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.613
(1.00) 		0.339
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.0577
(1.00) 		0.21
(1.00)
NCKAP5 13 (8%) 142 0.694
(1.00) 		0.918
(1.00) 		0.78
(1.00) 		0.433
(1.00) 		0.266
(1.00) 		0.568
(1.00) 		0.7
(1.00) 		0.817
(1.00) 		0.686
(1.00) 		0.889
(1.00)
C8B 9 (6%) 146 0.285
(1.00) 		0.159
(1.00) 		0.098
(1.00) 		0.152
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.636
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.999
(1.00)
DNAH5 28 (18%) 127 0.812
(1.00) 		0.839
(1.00) 		0.411
(1.00) 		0.771
(1.00) 		0.537
(1.00) 		0.37
(1.00) 		0.809
(1.00) 		0.23
(1.00) 		0.683
(1.00) 		0.0919
(1.00)
CCDC160 5 (3%) 150 0.777
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.144
(1.00) 		0.295
(1.00) 		0.548
(1.00) 		0.602
(1.00) 		0.535
(1.00) 		0.278
(1.00)
DCAF4L2 9 (6%) 146 0.951
(1.00) 		0.959
(1.00) 		1
(1.00) 		0.022
(1.00) 		0.0668
(1.00) 		0.799
(1.00) 		0.621
(1.00) 		0.812
(1.00) 		0.639
(1.00) 		0.453
(1.00)
DKK2 5 (3%) 150 0.727
(1.00) 		0.681
(1.00) 		0.582
(1.00) 		0.741
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.278
(1.00)
EPHA3 13 (8%) 142 0.455
(1.00) 		0.429
(1.00) 		0.402
(1.00) 		0.405
(1.00) 		0.468
(1.00) 		1
(1.00) 		1
(1.00) 		0.572
(1.00) 		0.686
(1.00) 		0.766
(1.00)
GUCY1A3 10 (6%) 145 0.11
(1.00) 		0.0668
(1.00) 		1
(1.00) 		0.0525
(1.00) 		0.17
(1.00) 		0.671
(1.00) 		0.4
(1.00) 		0.198
(1.00) 		0.651
(1.00) 		0.677
(1.00)
INHBA 7 (5%) 148 0.884
(1.00) 		0.474
(1.00) 		0.442
(1.00) 		0.00112
(1.00) 		0.169
(1.00) 		0.645
(1.00) 		0.613
(1.00) 		0.275
(1.00) 		0.633
(1.00) 		0.586
(1.00)
KLK2 3 (2%) 152 0.229
(1.00) 		1
(1.00) 		0.405
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.572
(1.00)
LPPR4 11 (7%) 144 0.592
(1.00) 		0.236
(1.00) 		0.765
(1.00) 		0.685
(1.00) 		0.411
(1.00) 		0.0266
(1.00) 		1
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.0669
(1.00)
OR7C1 6 (4%) 149 0.218
(1.00) 		0.442
(1.00) 		0.177
(1.00) 		0.274
(1.00) 		1
(1.00) 		1
(1.00) 		0.833
(1.00) 		1
(1.00) 		0.656
(1.00)
SCN7A 12 (8%) 143 0.6
(1.00) 		0.772
(1.00) 		0.564
(1.00) 		0.381
(1.00) 		0.0445
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.0171
(1.00) 		1
(1.00) 		0.951
(1.00)
TGFBR2 7 (5%) 148 0.768
(1.00) 		0.412
(1.00) 		0.719
(1.00) 		0.0791
(1.00) 		0.737
(1.00) 		0.565
(1.00) 		0.613
(1.00) 		0.753
(1.00) 		0.633
(1.00) 		0.789
(1.00)
TRPS1 13 (8%) 142 0.675
(1.00) 		0.153
(1.00) 		0.564
(1.00) 		0.127
(1.00) 		0.0628
(1.00) 		0.198
(1.00) 		0.281
(1.00) 		0.178
(1.00) 		0.463
(1.00) 		0.074
(1.00)
RIMS2 12 (8%) 143 0.228
(1.00) 		0.996
(1.00) 		0.564
(1.00) 		0.0985
(1.00) 		0.276
(1.00) 		0.919
(1.00) 		0.677
(1.00) 		0.576
(1.00) 		0.686
(1.00) 		0.504
(1.00)
SFMBT2 12 (8%) 143 0.379
(1.00) 		0.591
(1.00) 		0.765
(1.00) 		0.405
(1.00) 		0.241
(1.00) 		0.839
(1.00) 		0.677
(1.00) 		0.942
(1.00) 		0.686
(1.00) 		0.576
(1.00)
IL18R1 8 (5%) 147 0.497
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.113
(1.00) 		0.0803
(1.00) 		0.286
(1.00) 		0.621
(1.00) 		0.268
(1.00) 		0.633
(1.00) 		0.775
(1.00)
PCDH17 14 (9%) 141 0.181
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.699
(1.00) 		0.821
(1.00) 		0.147
(1.00) 		0.283
(1.00) 		0.104
(1.00) 		0.35
(1.00) 		0.0299
(1.00)
FLRT2 11 (7%) 144 0.64
(1.00) 		0.769
(1.00) 		0.368
(1.00) 		0.659
(1.00) 		0.0626
(1.00) 		0.691
(1.00) 		0.41
(1.00) 		0.274
(1.00) 		0.451
(1.00) 		0.14
(1.00)
ZC3H13 17 (11%) 138 0.841
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.0224
(1.00) 		0.209
(1.00) 		0.938
(1.00) 		0.221
(1.00) 		0.25
(1.00) 		0.368
(1.00) 		0.372
(1.00)
PTEN 4 (3%) 151 0.123
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.312
(1.00) 		0.819
(1.00) 		0.377
(1.00) 		0.415
(1.00) 		0.366
(1.00) 		0.492
(1.00)
NRXN3 15 (10%) 140 0.842
(1.00) 		0.485
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.883
(1.00) 		0.288
(1.00) 		0.291
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.0644
(1.00)
LIFR 13 (8%) 142 0.114
(1.00) 		0.666
(1.00) 		0.564
(1.00) 		0.433
(1.00) 		0.103
(1.00) 		0.786
(1.00) 		1
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.0389
(1.00)
OR2M2 6 (4%) 149 0.219
(1.00) 		0.428
(1.00) 		0.117
(1.00) 		0.0282
(1.00) 		0.0381
(1.00) 		1
(1.00) 		0.171
(1.00) 		0.204
(1.00) 		0.181
(1.00) 		0.198
(1.00)
TMEM132D 15 (10%) 140 0.91
(1.00) 		0.69
(1.00) 		0.186
(1.00) 		0.0639
(1.00) 		0.789
(1.00) 		0.56
(1.00) 		0.291
(1.00) 		0.0685
(1.00) 		0.35
(1.00) 		0.826
(1.00)
SAT1 4 (3%) 151 0.265
(1.00) 		0.0585
(1.00) 		0.501
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.869
(1.00)
CDH18 10 (6%) 145 0.179
(1.00) 		0.651
(1.00) 		0.0562
(1.00) 		0.659
(1.00) 		0.17
(1.00) 		0.477
(1.00) 		1
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.0115
(1.00)
P2RY10 6 (4%) 149 0.387
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.24
(1.00) 		0.689
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.0113
(1.00)
SYT16 6 (4%) 149 0.507
(1.00) 		0.587
(1.00) 		0.681
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.624
(1.00) 		0.612
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.646
(1.00)
CPXCR1 6 (4%) 149 0.327
(1.00) 		0.643
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.0178
(1.00) 		0.612
(1.00) 		0.232
(1.00) 		0.081
(1.00) 		0.0246
(1.00)
PDZRN4 12 (8%) 143 0.801
(1.00) 		0.159
(1.00) 		0.246
(1.00) 		0.00408
(1.00) 		0.276
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.858
(1.00) 		1
(1.00) 		0.337
(1.00)
ESR1 11 (7%) 144 0.439
(1.00) 		0.944
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.0296
(1.00) 		0.514
(1.00) 		0.401
(1.00) 		0.555
(1.00) 		0.651
(1.00) 		0.0575
(1.00)
MIER3 10 (6%) 145 0.463
(1.00) 		0.739
(1.00) 		0.534
(1.00) 		1
(1.00) 		0.555
(1.00) 		0.202
(1.00) 		0.4
(1.00) 		0.382
(1.00) 		0.651
(1.00) 		0.00232
(1.00)
NLRP5 10 (6%) 145 0.64
(1.00) 		0.794
(1.00) 		0.746
(1.00) 		0.634
(1.00) 		0.555
(1.00) 		0.283
(1.00) 		1
(1.00) 		0.414
(1.00) 		0.444
(1.00) 		0.42
(1.00)
PCDH10 14 (9%) 141 0.218
(1.00) 		0.327
(1.00) 		0.101
(1.00) 		0.239
(1.00) 		0.468
(1.00) 		0.63
(1.00) 		0.722
(1.00) 		0.502
(1.00) 		1
(1.00) 		0.447
(1.00)
PCDHB5 12 (8%) 143 0.0482
(1.00) 		0.831
(1.00) 		0.0788
(1.00) 		1
(1.00) 		0.204
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.0415
(1.00) 		0.463
(1.00) 		0.00645
(1.00)
TRPC6 8 (5%) 147 0.283
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.613
(1.00) 		0.458
(1.00) 		0.523
(1.00) 		0.621
(1.00) 		0.153
(1.00) 		0.633
(1.00) 		0.87
(1.00)
RHOA 4 (3%) 151 0.918
(1.00) 		1
(1.00) 		0.405
(1.00) 		0.741
(1.00) 		0.125
(1.00) 		0.469
(1.00) 		0.552
(1.00) 		0.457
(1.00) 		0.64
(1.00)
SYNE1 37 (24%) 118 0.773
(1.00) 		0.113
(1.00) 		0.576
(1.00) 		0.035
(1.00) 		0.591
(1.00) 		0.157
(1.00) 		0.544
(1.00) 		0.283
(1.00) 		0.741
(1.00) 		0.0154
(1.00)
CHRM2 8 (5%) 147 0.323
(1.00) 		0.778
(1.00) 		0.495
(1.00) 		0.613
(1.00) 		0.00611
(1.00) 		1
(1.00) 		0.131
(1.00) 		0.0187
(1.00) 		0.164
(1.00) 		0.939
(1.00)
GALNT14 9 (6%) 146 0.517
(1.00) 		0.996
(1.00) 		0.746
(1.00) 		0.634
(1.00) 		0.0103
(1.00) 		0.224
(1.00) 		0.4
(1.00) 		0.0203
(1.00) 		0.651
(1.00) 		0.339
(1.00)
LRRIQ3 7 (5%) 148 0.582
(1.00) 		0.495
(1.00) 		0.0633
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.903
(1.00) 		0.602
(1.00) 		0.59
(1.00)
PCDH11X 11 (7%) 144 0.0128
(1.00) 		0.561
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.183
(1.00) 		0.231
(1.00) 		0.401
(1.00) 		0.248
(1.00) 		0.444
(1.00) 		0.0694
(1.00)
TFAP2D 5 (3%) 150 0.0281
(1.00) 		0.21
(1.00) 		0.582
(1.00) 		0.784
(1.00) 		1
(1.00) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.87
(1.00)
CNTNAP4 10 (6%) 145 0.353
(1.00) 		0.936
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.17
(1.00) 		0.141
(1.00) 		0.4
(1.00) 		0.0203
(1.00) 		0.651
(1.00) 		0.752
(1.00)
DOCK2 16 (10%) 139 0.922
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.162
(1.00) 		0.212
(1.00) 		0.217
(1.00) 		0.0962
(1.00) 		0.357
(1.00) 		0.087
(1.00)
'BRAF MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.013

Table S1.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 128 24
BRAF MUTATED 9 11
BRAF WILD-TYPE 119 13

Figure S1.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'NRXN1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.76e-05 (t-test), Q value = 0.067

Table S2.  Gene #19: 'NRXN1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
NRXN1 MUTATED 17 0.4 (1.2)
NRXN1 WILD-TYPE 137 2.5 (4.7)

Figure S2.  Get High-res Image Gene #19: 'NRXN1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'ACVR2A MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-06 (t-test), Q value = 0.002

Table S3.  Gene #32: 'ACVR2A MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
ACVR2A MUTATED 8 0.2 (0.5)
ACVR2A WILD-TYPE 146 2.3 (4.6)

Figure S3.  Get High-res Image Gene #32: 'ACVR2A MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'CNBD1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.86e-09 (t-test), Q value = 6.9e-06

Table S4.  Gene #35: 'CNBD1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
CNBD1 MUTATED 6 0.0 (0.0)
CNBD1 WILD-TYPE 148 2.3 (4.5)

Figure S4.  Get High-res Image Gene #35: 'CNBD1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'BTNL8 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.1e-09 (t-test), Q value = 7.2e-06

Table S5.  Gene #44: 'BTNL8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
BTNL8 MUTATED 3 0.0 (0.0)
BTNL8 WILD-TYPE 151 2.3 (4.5)

Figure S5.  Get High-res Image Gene #44: 'BTNL8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'GGT1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.1e-09 (t-test), Q value = 7.2e-06

Table S6.  Gene #47: 'GGT1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
GGT1 MUTATED 3 0.0 (0.0)
GGT1 WILD-TYPE 151 2.3 (4.5)

Figure S6.  Get High-res Image Gene #47: 'GGT1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'GRIK3 MUTATION STATUS' versus 'AGE'

P value = 3.04e-05 (t-test), Q value = 0.036

Table S7.  Gene #52: 'GRIK3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 155 70.3 (12.0)
GRIK3 MUTATED 14 78.9 (5.8)
GRIK3 WILD-TYPE 141 69.5 (12.1)

Figure S7.  Get High-res Image Gene #52: 'GRIK3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'CASP8 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.26e-06 (t-test), Q value = 0.0027

Table S8.  Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
CASP8 MUTATED 10 0.2 (0.6)
CASP8 WILD-TYPE 144 2.4 (4.6)

Figure S8.  Get High-res Image Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'ERBB4 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.48e-06 (t-test), Q value = 0.0076

Table S9.  Gene #66: 'ERBB4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
ERBB4 MUTATED 14 0.3 (0.8)
ERBB4 WILD-TYPE 140 2.4 (4.6)

Figure S9.  Get High-res Image Gene #66: 'ERBB4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'IFT80 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.01e-07 (t-test), Q value = 0.00035

Table S10.  Gene #68: 'IFT80 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
IFT80 MUTATED 7 0.1 (0.4)
IFT80 WILD-TYPE 147 2.3 (4.6)

Figure S10.  Get High-res Image Gene #68: 'IFT80 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'OR8J1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.02e-09 (t-test), Q value = 7.1e-06

Table S11.  Gene #76: 'OR8J1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
OR8J1 MUTATED 4 0.0 (0.0)
OR8J1 WILD-TYPE 150 2.3 (4.5)

Figure S11.  Get High-res Image Gene #76: 'OR8J1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'ZFHX4 MUTATION STATUS' versus 'Time to Death'

P value = 2.48e-05 (logrank test), Q value = 0.029

Table S12.  Gene #84: 'ZFHX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 79 11 0.9 - 52.0 (12.0)
ZFHX4 MUTATED 11 4 0.9 - 21.0 (1.0)
ZFHX4 WILD-TYPE 68 7 0.9 - 52.0 (13.9)

Figure S12.  Get High-res Image Gene #84: 'ZFHX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ZNF429 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.00011 (t-test), Q value = 0.13

Table S13.  Gene #87: 'ZNF429 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
ZNF429 MUTATED 7 0.3 (0.8)
ZNF429 WILD-TYPE 147 2.3 (4.6)

Figure S13.  Get High-res Image Gene #87: 'ZNF429 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'DKK4 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.02e-09 (t-test), Q value = 7.1e-06

Table S14.  Gene #94: 'DKK4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
DKK4 MUTATED 4 0.0 (0.0)
DKK4 WILD-TYPE 150 2.3 (4.5)

Figure S14.  Get High-res Image Gene #94: 'DKK4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'NALCN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.79e-05 (t-test), Q value = 0.079

Table S15.  Gene #95: 'NALCN MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
NALCN MUTATED 14 0.4 (1.1)
NALCN WILD-TYPE 140 2.4 (4.6)

Figure S15.  Get High-res Image Gene #95: 'NALCN MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'SULT1C4 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.1e-09 (t-test), Q value = 7.2e-06

Table S16.  Gene #96: 'SULT1C4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
SULT1C4 MUTATED 3 0.0 (0.0)
SULT1C4 WILD-TYPE 151 2.3 (4.5)

Figure S16.  Get High-res Image Gene #96: 'SULT1C4 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'UMOD MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.00011 (t-test), Q value = 0.13

Table S17.  Gene #97: 'UMOD MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
UMOD MUTATED 7 0.3 (0.8)
UMOD WILD-TYPE 147 2.3 (4.6)

Figure S17.  Get High-res Image Gene #97: 'UMOD MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'USP17L2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.78e-09 (t-test), Q value = 6.9e-06

Table S18.  Gene #100: 'USP17L2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
USP17L2 MUTATED 7 0.0 (0.0)
USP17L2 WILD-TYPE 147 2.3 (4.6)

Figure S18.  Get High-res Image Gene #100: 'USP17L2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'FAM5C MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.21e-08 (t-test), Q value = 6.1e-05

Table S19.  Gene #102: 'FAM5C MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
FAM5C MUTATED 10 0.1 (0.3)
FAM5C WILD-TYPE 144 2.4 (4.6)

Figure S19.  Get High-res Image Gene #102: 'FAM5C MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'OR6T1 MUTATION STATUS' versus 'AGE'

P value = 0.000122 (t-test), Q value = 0.14

Table S20.  Gene #105: 'OR6T1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 155 70.3 (12.0)
OR6T1 MUTATED 6 63.7 (2.5)
OR6T1 WILD-TYPE 149 70.6 (12.2)

Figure S20.  Get High-res Image Gene #105: 'OR6T1 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'CYTL1 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.02e-09 (t-test), Q value = 7.1e-06

Table S21.  Gene #111: 'CYTL1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
CYTL1 MUTATED 4 0.0 (0.0)
CYTL1 WILD-TYPE 150 2.3 (4.5)

Figure S21.  Get High-res Image Gene #111: 'CYTL1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'NAALAD2 MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.34e-05 (t-test), Q value = 0.039

Table S22.  Gene #115: 'NAALAD2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
NAALAD2 MUTATED 11 0.4 (0.8)
NAALAD2 WILD-TYPE 143 2.4 (4.6)

Figure S22.  Get High-res Image Gene #115: 'NAALAD2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'TNR MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.39e-06 (t-test), Q value = 0.0016

Table S23.  Gene #118: 'TNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 154 2.2 (4.5)
TNR MUTATED 15 0.2 (0.8)
TNR WILD-TYPE 139 2.4 (4.7)

Figure S23.  Get High-res Image Gene #118: 'TNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

  • Clinical data file = COAD-TP.clin.merged.picked.txt

  • Number of patients = 155

  • Number of significantly mutated genes = 120

  • Number of selected clinical features = 10

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

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] 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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