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 111 genes and 8 clinical features across 161 patients, 9 significant findings detected with Q value < 0.25.

  • OXA1L mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • PTEN mutation correlated to 'DISTANT.METASTASIS'.

  • MUC7 mutation correlated to 'AGE'.

  • RAPGEF5 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • ANKRD20A4 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • C9ORF119 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • C2 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • SPINK13 mutation correlated to 'LYMPH.NODE.METASTASIS'.

  • GNAI2 mutation correlated to 'LYMPH.NODE.METASTASIS'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 111 genes and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		GENDER DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nMutated (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Chi-square test Chi-square test t-test Chi-square test
OXA1L 5 (3%) 156 0.695
(1.00) 		0.613
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.00012
(0.0914) 		0.48
(1.00)
PTEN 13 (8%) 148 0.703
(1.00) 		0.234
(1.00) 		0.473
(1.00) 		0.551
(1.00) 		0.00028
(0.213) 		0.835
(1.00) 		0.0325
(1.00)
MUC7 11 (7%) 150 0.36
(1.00) 		0.000223
(0.17) 		0.819
(1.00) 		0.747
(1.00) 		0.964
(1.00) 		0.828
(1.00) 		0.576
(1.00)
RAPGEF5 8 (5%) 153 0.997
(1.00) 		0.36
(1.00) 		0.1
(1.00) 		0.26
(1.00) 		0.989
(1.00) 		0.000279
(0.212) 		0.331
(1.00)
ANKRD20A4 4 (2%) 157 0.449
(1.00) 		0.531
(1.00) 		0.778
(1.00) 		0.297
(1.00) 		0.995
(1.00) 		1.62e-05
(0.0124) 		0.564
(1.00)
C9ORF119 5 (3%) 156 0.333
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.992
(1.00) 		5.91e-05
(0.0451) 		0.817
(1.00)
C2 7 (4%) 154 0.485
(1.00) 		0.883
(1.00) 		0.742
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.000172
(0.131) 		0.349
(1.00)
SPINK13 6 (4%) 155 0.0886
(1.00) 		0.168
(1.00) 		0.84
(1.00) 		0.416
(1.00) 		0.989
(1.00) 		3.89e-05
(0.0297) 		0.817
(1.00)
GNAI2 4 (2%) 157 0.133
(1.00) 		0.531
(1.00) 		0.44
(1.00) 		0.624
(1.00) 		0.997
(1.00) 		3.35e-09
(2.57e-06) 		0.572
(1.00)
TP53 26 (16%) 135 0.687
(1.00) 		0.07
(1.00) 		0.221
(1.00) 		0.828
(1.00) 		0.59
(1.00) 		0.0964
(1.00) 		0.464
(1.00)
BRAF 82 (51%) 79 0.256
(1.00) 		0.0963
(1.00) 		0.126
(1.00) 		0.746
(1.00) 		0.568
(1.00) 		0.835
(1.00) 		0.635
(1.00)
C15ORF23 11 (7%) 150 0.579
(1.00) 		0.67
(1.00) 		0.819
(1.00) 		0.747
(1.00) 		0.97
(1.00) 		0.488
(1.00) 		0.679
(1.00)
CDKN2A 27 (17%) 134 0.571
(1.00) 		0.995
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.746
(1.00) 		0.366
(1.00)
NRAS 49 (30%) 112 0.7
(1.00) 		0.394
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.618
(1.00) 		0.91
(1.00) 		0.591
(1.00)
STK19 10 (6%) 151 0.415
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.5
(1.00) 		0.975
(1.00) 		0.965
(1.00) 		0.76
(1.00)
RAC1 12 (7%) 149 0.0898
(1.00) 		0.415
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.895
(1.00) 		0.303
(1.00)
IDH1 8 (5%) 153 0.697
(1.00) 		0.00483
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.981
(1.00) 		0.981
(1.00) 		0.703
(1.00)
ACSM2B 31 (19%) 130 0.352
(1.00) 		0.861
(1.00) 		0.0877
(1.00) 		0.00183
(1.00) 		0.771
(1.00) 		0.351
(1.00) 		0.822
(1.00)
PPP6C 15 (9%) 146 0.00412
(1.00) 		0.647
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.0481
(1.00) 		0.755
(1.00)
LCE1B 9 (6%) 152 0.0619
(1.00) 		0.75
(1.00) 		0.0817
(1.00) 		0.726
(1.00) 		0.981
(1.00) 		0.933
(1.00) 		0.674
(1.00)
OR51S1 17 (11%) 144 0.668
(1.00) 		0.424
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.0496
(1.00) 		0.201
(1.00)
NAP1L2 17 (11%) 144 0.29
(1.00) 		0.0518
(1.00) 		0.0722
(1.00) 		0.426
(1.00) 		0.925
(1.00) 		0.0605
(1.00) 		0.635
(1.00)
PRB2 24 (15%) 137 0.528
(1.00) 		0.00385
(1.00) 		0.158
(1.00) 		0.0374
(1.00) 		0.862
(1.00) 		0.412
(1.00) 		0.287
(1.00)
TAF1A 10 (6%) 151 0.107
(1.00) 		0.57
(1.00) 		0.893
(1.00) 		0.5
(1.00) 		0.179
(1.00) 		0.733
(1.00) 		0.823
(1.00)
HIST1H2AA 7 (4%) 154 0.734
(1.00) 		0.975
(1.00) 		0.0409
(1.00) 		0.708
(1.00) 		0.985
(1.00) 		0.955
(1.00) 		0.751
(1.00)
FRG2B 10 (6%) 151 0.639
(1.00) 		0.0224
(1.00) 		0.808
(1.00) 		0.5
(1.00) 		0.97
(1.00) 		0.916
(1.00) 		0.566
(1.00)
CDH9 27 (17%) 134 0.245
(1.00) 		0.385
(1.00) 		0.0132
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.204
(1.00) 		0.0904
(1.00)
PRAMEF11 15 (9%) 146 0.0347
(1.00) 		0.0848
(1.00) 		0.751
(1.00) 		0.784
(1.00) 		0.942
(1.00) 		0.0513
(1.00) 		0.854
(1.00)
HBG2 7 (4%) 154 0.486
(1.00) 		0.156
(1.00) 		0.854
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.00722
(1.00) 		0.758
(1.00)
DDX3X 16 (10%) 145 0.57
(1.00) 		0.538
(1.00) 		0.54
(1.00) 		0.172
(1.00) 		0.00456
(1.00) 		0.991
(1.00) 		0.704
(1.00)
PRB4 18 (11%) 143 0.0555
(1.00) 		0.123
(1.00) 		0.307
(1.00) 		0.205
(1.00) 		0.438
(1.00) 		0.12
(1.00) 		0.874
(1.00)
GRXCR1 15 (9%) 146 0.178
(1.00) 		0.0286
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.78
(1.00) 		0.318
(1.00)
HHLA2 12 (7%) 149 0.723
(1.00) 		0.301
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.0249
(1.00) 		0.908
(1.00)
RBM11 11 (7%) 150 0.526
(1.00) 		0.194
(1.00) 		0.673
(1.00) 		0.747
(1.00) 		0.227
(1.00) 		0.0329
(1.00) 		0.367
(1.00)
FUT9 17 (11%) 144 0.291
(1.00) 		0.0352
(1.00) 		0.389
(1.00) 		0.602
(1.00) 		0.916
(1.00) 		0.157
(1.00) 		0.256
(1.00)
TTN 127 (79%) 34 0.186
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.496
(1.00) 		0.353
(1.00) 		0.376
(1.00)
HBD 9 (6%) 152 0.0883
(1.00) 		0.856
(1.00) 		0.376
(1.00) 		0.726
(1.00) 		0.975
(1.00) 		0.945
(1.00) 		0.349
(1.00)
KIAA1257 7 (4%) 154 0.22
(1.00) 		0.333
(1.00) 		0.538
(1.00) 		0.424
(1.00) 		0.992
(1.00) 		0.885
(1.00) 		0.729
(1.00)
USP17L2 16 (10%) 145 0.93
(1.00) 		0.662
(1.00) 		0.0759
(1.00) 		0.172
(1.00) 		0.934
(1.00) 		0.145
(1.00) 		0.113
(1.00)
CADM2 18 (11%) 143 0.432
(1.00) 		0.944
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.906
(1.00) 		0.136
(1.00) 		0.409
(1.00)
GFRAL 24 (15%) 137 0.971
(1.00) 		0.82
(1.00) 		0.177
(1.00) 		0.82
(1.00) 		0.59
(1.00) 		0.122
(1.00) 		0.0761
(1.00)
OR4N2 19 (12%) 142 0.824
(1.00) 		0.363
(1.00) 		0.189
(1.00) 		0.0112
(1.00) 		0.0769
(1.00) 		0.277
(1.00) 		0.663
(1.00)
UGT2B15 17 (11%) 144 0.647
(1.00) 		0.36
(1.00) 		0.773
(1.00) 		0.112
(1.00) 		0.117
(1.00) 		0.126
(1.00) 		0.14
(1.00)
UNC119B 3 (2%) 158 0.999
(1.00) 		0.375
(1.00) 		1
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.99
(1.00) 		0.555
(1.00)
C8A 21 (13%) 140 0.497
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.0906
(1.00) 		0.0914
(1.00) 		0.38
(1.00) 		0.426
(1.00)
ELF5 4 (2%) 157 0.562
(1.00) 		0.775
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.28
(1.00) 		0.97
(1.00)
SPAG16 13 (8%) 148 0.501
(1.00) 		0.753
(1.00) 		0.848
(1.00) 		0.377
(1.00) 		0.964
(1.00) 		0.0615
(1.00) 		0.582
(1.00)
PHGDH 8 (5%) 153 0.776
(1.00) 		0.695
(1.00) 		0.588
(1.00) 		0.0273
(1.00) 		0.989
(1.00) 		0.00217
(1.00) 		0.143
(1.00)
COPG2 3 (2%) 158 0.454
(1.00) 		0.997
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.99
(1.00) 		0.0442
(1.00)
GML 8 (5%) 153 0.898
(1.00) 		0.114
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.985
(1.00) 		0.746
(1.00) 		0.965
(1.00)
TBC1D3B 3 (2%) 158 0.00198
(1.00) 		0.404
(1.00) 		0.285
(1.00) 		1
(1.00)
TFEC 15 (9%) 146 0.37
(1.00) 		0.111
(1.00) 		1
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.00562
(1.00) 		0.571
(1.00)
TRAT1 11 (7%) 150 0.0369
(1.00) 		0.545
(1.00) 		0.0648
(1.00) 		0.533
(1.00) 		0.97
(1.00) 		0.0218
(1.00) 		0.86
(1.00)
PRR23B 11 (7%) 150 0.206
(1.00) 		0.813
(1.00) 		0.0825
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.042
(1.00) 		0.907
(1.00)
LIN7A 9 (6%) 152 0.647
(1.00) 		0.581
(1.00) 		0.376
(1.00) 		0.488
(1.00) 		0.985
(1.00) 		0.00709
(1.00) 		0.576
(1.00)
PARM1 14 (9%) 147 0.288
(1.00) 		0.234
(1.00) 		0.283
(1.00) 		0.577
(1.00) 		0.95
(1.00) 		0.00212
(1.00) 		0.167
(1.00)
CCK 5 (3%) 156 0.112
(1.00) 		0.725
(1.00) 		0.656
(1.00) 		0.653
(1.00) 		0.995
(1.00) 		0.024
(1.00) 		0.795
(1.00)
TCEB3C 23 (14%) 138 0.334
(1.00) 		0.472
(1.00) 		0.864
(1.00) 		0.16
(1.00) 		0.862
(1.00) 		0.533
(1.00) 		0.458
(1.00)
DEFB118 7 (4%) 154 0.0924
(1.00) 		0.64
(1.00) 		0.742
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.0094
(1.00) 		0.762
(1.00)
VEGFC 16 (10%) 145 0.93
(1.00) 		0.899
(1.00) 		0.394
(1.00) 		0.589
(1.00) 		0.942
(1.00) 		0.0142
(1.00) 		0.331
(1.00)
MARCH11 8 (5%) 153 0.226
(1.00) 		0.789
(1.00) 		0.208
(1.00) 		0.711
(1.00) 		0.0895
(1.00) 		0.0156
(1.00) 		0.289
(1.00)
ZFP106 6 (4%) 155 0.524
(1.00) 		0.000615
(0.466) 		0.491
(1.00) 		0.0864
(1.00) 		0.989
(1.00) 		0.81
(1.00) 		0.382
(1.00)
PDE1A 26 (16%) 135 0.666
(1.00) 		0.13
(1.00) 		0.0187
(1.00) 		0.657
(1.00) 		0.838
(1.00) 		0.136
(1.00) 		0.708
(1.00)
OR4F6 12 (7%) 149 0.319
(1.00) 		0.202
(1.00) 		0.916
(1.00) 		0.538
(1.00) 		0.227
(1.00) 		0.0866
(1.00) 		0.585
(1.00)
CD2 15 (9%) 146 0.387
(1.00) 		0.261
(1.00) 		0.0406
(1.00) 		0.784
(1.00) 		0.0891
(1.00) 		0.182
(1.00) 		0.439
(1.00)
EIF3D 3 (2%) 158 0.0444
(1.00) 		0.481
(1.00) 		0.725
(1.00) 		0.299
(1.00) 		0.997
(1.00) 		0.979
(1.00) 		0.628
(1.00)
MKX 11 (7%) 150 0.373
(1.00) 		0.684
(1.00) 		0.0593
(1.00) 		0.747
(1.00) 		0.981
(1.00) 		0.0156
(1.00) 		0.0422
(1.00)
ARL16 5 (3%) 156 0.212
(1.00) 		0.0271
(1.00) 		0.0592
(1.00) 		0.653
(1.00) 		0.992
(1.00) 		0.885
(1.00) 		0.157
(1.00)
OR2L3 13 (8%) 148 0.999
(1.00) 		0.928
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0189
(1.00) 		0.057
(1.00) 		0.0699
(1.00)
DEFB119 6 (4%) 155 0.19
(1.00) 		0.188
(1.00) 		0.155
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.943
(1.00) 		0.513
(1.00)
KLHL4 16 (10%) 145 0.0678
(1.00) 		0.902
(1.00) 		0.252
(1.00) 		0.589
(1.00) 		0.95
(1.00) 		0.124
(1.00) 		0.59
(1.00)
NR1H4 10 (6%) 151 0.381
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.975
(1.00) 		0.0042
(1.00) 		0.363
(1.00)
IL32 7 (4%) 154 0.0335
(1.00) 		0.702
(1.00) 		0.538
(1.00) 		0.708
(1.00) 		0.985
(1.00) 		0.833
(1.00) 		0.00832
(1.00)
DGAT2L6 9 (6%) 152 0.368
(1.00) 		0.349
(1.00) 		0.0312
(1.00) 		1
(1.00) 		0.975
(1.00) 		0.0113
(1.00) 		0.762
(1.00)
OR8D4 9 (6%) 152 0.035
(1.00) 		0.625
(1.00) 		0.482
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.014
(1.00) 		0.967
(1.00)
GRXCR2 12 (7%) 149 0.268
(1.00) 		0.951
(1.00) 		0.055
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.0342
(1.00) 		0.683
(1.00)
OR5H2 12 (7%) 149 0.293
(1.00) 		0.0158
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.957
(1.00) 		0.023
(1.00) 		0.515
(1.00)
SIGLEC14 8 (5%) 153 0.724
(1.00) 		0.042
(1.00) 		0.118
(1.00) 		0.0273
(1.00) 		0.985
(1.00) 		0.0094
(1.00) 		0.42
(1.00)
ZNF479 15 (9%) 146 0.313
(1.00) 		0.267
(1.00) 		0.806
(1.00) 		0.784
(1.00) 		0.362
(1.00) 		0.125
(1.00) 		0.785
(1.00)
GH2 10 (6%) 151 0.547
(1.00) 		0.483
(1.00) 		0.466
(1.00) 		0.747
(1.00) 		0.981
(1.00) 		0.00432
(1.00) 		0.0533
(1.00)
GK2 21 (13%) 140 0.206
(1.00) 		0.727
(1.00) 		0.105
(1.00) 		1
(1.00) 		0.896
(1.00) 		0.0829
(1.00) 		0.0679
(1.00)
C2ORF40 4 (2%) 157 0.84
(1.00) 		0.404
(1.00) 		0.0637
(1.00) 		0.624
(1.00) 		0.997
(1.00) 		0.979
(1.00)
CXCR2 11 (7%) 150 0.0546
(1.00) 		0.675
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.0472
(1.00) 		0.269
(1.00)
RPTN 27 (17%) 134 0.252
(1.00) 		0.165
(1.00) 		0.062
(1.00) 		0.513
(1.00) 		0.838
(1.00) 		0.0846
(1.00) 		0.0456
(1.00)
PRIM2 9 (6%) 152 0.279
(1.00) 		0.5
(1.00) 		0.299
(1.00) 		0.156
(1.00) 		0.132
(1.00) 		0.0067
(1.00) 		0.0239
(1.00)
MUM1L1 17 (11%) 144 0.4
(1.00) 		0.675
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.0802
(1.00) 		0.349
(1.00)
TLL1 33 (20%) 128 0.941
(1.00) 		0.169
(1.00) 		0.293
(1.00) 		0.426
(1.00) 		0.674
(1.00) 		0.146
(1.00) 		0.405
(1.00)
PRC1 9 (6%) 152 0.635
(1.00) 		0.445
(1.00) 		0.551
(1.00) 		0.488
(1.00) 		0.981
(1.00) 		0.717
(1.00) 		0.931
(1.00)
GLRB 19 (12%) 142 0.612
(1.00) 		0.189
(1.00) 		0.0396
(1.00) 		0.801
(1.00) 		0.896
(1.00) 		0.241
(1.00) 		0.818
(1.00)
AREG 6 (4%) 155 0.491
(1.00) 		0.294
(1.00) 		0.84
(1.00) 		0.67
(1.00) 		0.992
(1.00) 		0.000342
(0.259) 		0.454
(1.00)
ACD 7 (4%) 154 0.912
(1.00) 		0.563
(1.00) 		0.0286
(1.00) 		0.424
(1.00) 		0.985
(1.00) 		0.00442
(1.00) 		0.384
(1.00)
C2ORF39 8 (5%) 153 0.583
(1.00) 		0.22
(1.00) 		1
(1.00) 		0.711
(1.00) 		0.053
(1.00) 		0.00709
(1.00) 		0.576
(1.00)
RERG 9 (6%) 152 0.669
(1.00) 		0.0961
(1.00) 		0.482
(1.00) 		0.488
(1.00) 		0.985
(1.00) 		0.0016
(1.00) 		0.438
(1.00)
TUBB8 8 (5%) 153 0.691
(1.00) 		0.352
(1.00) 		1
(1.00) 		0.711
(1.00) 		0.989
(1.00) 		0.00217
(1.00) 		0.693
(1.00)
AGXT2 16 (10%) 145 0.353
(1.00) 		0.386
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.113
(1.00) 		0.611
(1.00)
C9 12 (7%) 149 0.705
(1.00) 		0.679
(1.00) 		0.834
(1.00) 		0.76
(1.00) 		0.97
(1.00) 		0.0321
(1.00) 		0.901
(1.00)
CX3CL1 3 (2%) 158 0.427
(1.00) 		0.938
(1.00) 		0.469
(1.00) 		1
(1.00)
DEFB112 6 (4%) 155 0.236
(1.00) 		0.462
(1.00) 		0.0332
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.00157
(1.00) 		0.727
(1.00)
FAM19A1 7 (4%) 154 0.433
(1.00) 		0.964
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.989
(1.00) 		0.76
(1.00) 		0.813
(1.00)
LONRF2 13 (8%) 148 0.0182
(1.00) 		0.885
(1.00) 		0.558
(1.00) 		0.77
(1.00) 		0.975
(1.00) 		0.297
(1.00) 		0.458
(1.00)
NAP1L4 6 (4%) 155 0.326
(1.00) 		0.34
(1.00) 		0.84
(1.00) 		0.67
(1.00) 		0.989
(1.00) 		0.628
(1.00) 		0.606
(1.00)
OR5J2 11 (7%) 150 0.673
(1.00) 		0.757
(1.00) 		0.673
(1.00) 		0.213
(1.00) 		0.975
(1.00) 		0.996
(1.00) 		0.833
(1.00)
POM121 11 (7%) 150 0.258
(1.00) 		0.984
(1.00) 		0.338
(1.00) 		0.747
(1.00) 		0.97
(1.00) 		0.0371
(1.00) 		0.0149
(1.00)
RBM22 4 (2%) 157 0.733
(1.00) 		0.327
(1.00) 		0.6
(1.00) 		0.297
(1.00) 		0.995
(1.00) 		0.985
(1.00) 		0.721
(1.00)
SLC10A2 15 (9%) 146 0.494
(1.00) 		0.238
(1.00) 		0.154
(1.00) 		0.784
(1.00) 		0.942
(1.00) 		0.032
(1.00) 		0.0825
(1.00)
C4ORF22 8 (5%) 153 0.693
(1.00) 		0.545
(1.00) 		0.281
(1.00) 		0.711
(1.00) 		0.985
(1.00) 		0.993
(1.00) 		0.771
(1.00)
CLEC14A 15 (9%) 146 0.183
(1.00) 		0.926
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.957
(1.00) 		0.0304
(1.00) 		0.422
(1.00)
IGF2BP3 3 (2%) 158 0.854
(1.00) 		0.687
(1.00) 		0.469
(1.00) 		1
(1.00)
RBM46 11 (7%) 150 0.998
(1.00) 		0.134
(1.00) 		0.0703
(1.00) 		0.533
(1.00) 		0.964
(1.00) 		0.0653
(1.00) 		0.829
(1.00)
SERPINB4 21 (13%) 140 0.928
(1.00) 		0.209
(1.00) 		0.378
(1.00) 		0.0278
(1.00) 		0.121
(1.00) 		0.348
(1.00) 		0.902
(1.00)
SORT1 5 (3%) 156 0.34
(1.00) 		0.6
(1.00) 		0.0592
(1.00) 		0.653
(1.00) 		0.992
(1.00) 		0.696
(1.00) 		0.147
(1.00)
'OXA1L MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 0.00012 (Chi-square test), Q value = 0.091

Table S1.  Gene #6: 'OXA1L MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
OXA1L MUTATED 2 0 1 1 1 0 0 0 0 0
OXA1L WILD-TYPE 86 2 6 14 0 4 10 5 15 1

Figure S1.  Get High-res Image Gene #6: 'OXA1L MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'PTEN MUTATION STATUS' versus 'DISTANT.METASTASIS'

P value = 0.00028 (Chi-square test), Q value = 0.21

Table S2.  Gene #8: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B M1C
ALL 140 2 1 2 2
PTEN MUTATED 11 2 0 0 0
PTEN WILD-TYPE 129 0 1 2 2

Figure S2.  Get High-res Image Gene #8: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'DISTANT.METASTASIS'

'MUC7 MUTATION STATUS' versus 'AGE'

P value = 0.000223 (t-test), Q value = 0.17

Table S3.  Gene #14: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 160 56.3 (15.8)
MUC7 MUTATED 11 72.7 (10.9)
MUC7 WILD-TYPE 149 55.1 (15.5)

Figure S3.  Get High-res Image Gene #14: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'RAPGEF5 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000279 (Chi-square test), Q value = 0.21

Table S4.  Gene #39: 'RAPGEF5 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
RAPGEF5 MUTATED 2 0 1 2 1 0 0 0 0 0
RAPGEF5 WILD-TYPE 86 2 6 13 0 4 10 5 15 1

Figure S4.  Get High-res Image Gene #39: 'RAPGEF5 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'ANKRD20A4 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 1.62e-05 (Chi-square test), Q value = 0.012

Table S5.  Gene #41: 'ANKRD20A4 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
ANKRD20A4 MUTATED 2 0 0 1 1 0 0 0 0 0
ANKRD20A4 WILD-TYPE 86 2 7 14 0 4 10 5 15 1

Figure S5.  Get High-res Image Gene #41: 'ANKRD20A4 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'C9ORF119 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 5.91e-05 (Chi-square test), Q value = 0.045

Table S6.  Gene #51: 'C9ORF119 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
C9ORF119 MUTATED 2 0 0 2 1 0 0 0 0 0
C9ORF119 WILD-TYPE 86 2 7 13 0 4 10 5 15 1

Figure S6.  Get High-res Image Gene #51: 'C9ORF119 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'C2 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000172 (Chi-square test), Q value = 0.13

Table S7.  Gene #77: 'C2 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
C2 MUTATED 3 0 0 0 1 0 2 0 0 0
C2 WILD-TYPE 85 2 7 15 0 4 8 5 15 1

Figure S7.  Get High-res Image Gene #77: 'C2 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'SPINK13 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 3.89e-05 (Chi-square test), Q value = 0.03

Table S8.  Gene #89: 'SPINK13 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
SPINK13 MUTATED 2 0 0 3 1 0 0 0 0 0
SPINK13 WILD-TYPE 86 2 7 12 0 4 10 5 15 1

Figure S8.  Get High-res Image Gene #89: 'SPINK13 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'GNAI2 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 3.35e-09 (Chi-square test), Q value = 2.6e-06

Table S9.  Gene #107: 'GNAI2 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 88 2 7 15 1 4 10 5 15 1
GNAI2 MUTATED 1 0 0 0 1 0 0 1 0 0
GNAI2 WILD-TYPE 87 2 7 15 0 4 10 4 15 1

Figure S9.  Get High-res Image Gene #107: 'GNAI2 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

Methods & Data
Input

  • Mutation data file = SKCM-All_Metastatic.mutsig.cluster.txt

  • Clinical data file = SKCM-All_Metastatic.clin.merged.picked.txt

  • Number of patients = 161

  • Number of significantly mutated genes = 111

  • Number of selected clinical features = 8

  • 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

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] 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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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