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 106 genes and 9 clinical features across 184 patients, 9 significant findings detected with Q value < 0.25.

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

  • MUC7 mutation correlated to 'AGE'.

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

  • ZMAT4 mutation correlated to 'LYMPH.NODE.METASTASIS'.

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

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 106 genes and 9 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 RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nMutated (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Chi-square test t-test Chi-square test
OXA1L 5 (3%) 179 0.638
(1.00) 		0.633
(1.00) 		0.73
(1.00) 		1
(1.00) 		1
(1.00) 		0.992
(1.00) 		1.73e-05
(0.0145) 		0.404
(1.00)
MUC7 11 (6%) 173 0.306
(1.00) 		0.000286
(0.238) 		0.701
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.767
(1.00) 		0.454
(1.00)
ANKRD20A4 4 (2%) 180 0.415
(1.00) 		0.574
(1.00) 		0.862
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.995
(1.00) 		1.35e-06
(0.00113) 		0.453
(1.00)
ZMAT4 5 (3%) 179 0.244
(1.00) 		0.000375
(0.312) 		0.196
(1.00) 		0.656
(1.00) 		0.0797
(1.00) 		0.992
(1.00) 		8.12e-06
(0.0068) 		0.926
(1.00)
C9ORF119 5 (3%) 179 0.309
(1.00) 		0.354
(1.00) 		1
(1.00) 		0.162
(1.00) 		1
(1.00) 		0.992
(1.00) 		5.79e-06
(0.00486) 		0.757
(1.00)
SPINK13 6 (3%) 178 0.116
(1.00) 		0.181
(1.00) 		0.918
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.989
(1.00) 		3.33e-06
(0.00279) 		0.743
(1.00)
RAPGEF5 9 (5%) 175 0.93
(1.00) 		0.415
(1.00) 		0.15
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.985
(1.00) 		5.24e-05
(0.0438) 		0.385
(1.00)
GNAI2 4 (2%) 180 0.178
(1.00) 		0.505
(1.00) 		0.657
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.997
(1.00) 		1.55e-10
(1.31e-07) 		0.443
(1.00)
AREG 6 (3%) 178 0.452
(1.00) 		0.281
(1.00) 		0.918
(1.00) 		0.668
(1.00) 		1
(1.00) 		0.992
(1.00) 		5.86e-05
(0.0489) 		0.339
(1.00)
BRAF 98 (53%) 86 0.312
(1.00) 		0.0806
(1.00) 		0.0393
(1.00) 		0.54
(1.00) 		0.1
(1.00) 		0.481
(1.00) 		0.637
(1.00) 		0.455
(1.00)
C15ORF23 11 (6%) 173 0.516
(1.00) 		0.707
(1.00) 		0.701
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.362
(1.00) 		0.506
(1.00)
CDKN2A 28 (15%) 156 0.726
(1.00) 		0.999
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.392
(1.00) 		0.832
(1.00) 		0.67
(1.00) 		0.266
(1.00)
NRAS 52 (28%) 132 0.944
(1.00) 		0.568
(1.00) 		0.0922
(1.00) 		1
(1.00) 		0.56
(1.00) 		0.575
(1.00) 		0.738
(1.00) 		0.459
(1.00)
STK19 10 (5%) 174 0.486
(1.00) 		0.315
(1.00) 		0.844
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.969
(1.00) 		0.674
(1.00)
TP53 29 (16%) 155 0.668
(1.00) 		0.0284
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.794
(1.00) 		0.11
(1.00) 		0.643
(1.00)
TTN 144 (78%) 40 0.195
(1.00) 		0.832
(1.00) 		0.91
(1.00) 		0.195
(1.00) 		0.523
(1.00) 		0.64
(1.00) 		0.442
(1.00) 		0.174
(1.00)
UGT2B15 18 (10%) 166 0.558
(1.00) 		0.611
(1.00) 		0.703
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.0326
(1.00) 		0.119
(1.00)
PTEN 17 (9%) 167 0.641
(1.00) 		0.372
(1.00) 		0.936
(1.00) 		0.608
(1.00) 		0.254
(1.00) 		0.000969
(0.803) 		0.686
(1.00) 		0.168
(1.00)
RAC1 12 (7%) 172 0.128
(1.00) 		0.45
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.97
(1.00) 		0.895
(1.00) 		0.609
(1.00)
PPP6C 18 (10%) 166 0.00329
(1.00) 		0.936
(1.00) 		0.978
(1.00) 		1
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.0698
(1.00) 		0.877
(1.00)
PRB2 28 (15%) 156 0.404
(1.00) 		0.00198
(1.00) 		0.117
(1.00) 		0.0915
(1.00) 		1
(1.00) 		0.82
(1.00) 		0.146
(1.00) 		0.162
(1.00)
IDH1 10 (5%) 174 0.912
(1.00) 		0.2
(1.00) 		0.752
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.359
(1.00) 		0.942
(1.00) 		0.688
(1.00)
NAP1L2 18 (10%) 166 0.216
(1.00) 		0.251
(1.00) 		0.624
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.0506
(1.00) 		0.561
(1.00)
FIGLA 3 (2%) 181 0.0444
(1.00) 		0.507
(1.00) 		0.816
(1.00) 		0.554
(1.00) 		0.0484
(1.00) 		0.928
(1.00)
RBM11 13 (7%) 171 0.625
(1.00) 		0.101
(1.00) 		0.658
(1.00) 		0.384
(1.00) 		0.198
(1.00) 		0.527
(1.00) 		0.0486
(1.00) 		0.566
(1.00)
HBG2 7 (4%) 177 0.436
(1.00) 		0.168
(1.00) 		0.871
(1.00) 		1
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.0022
(1.00) 		0.823
(1.00)
LCE1B 9 (5%) 175 0.0861
(1.00) 		0.708
(1.00) 		0.95
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.923
(1.00) 		0.511
(1.00)
DDX3X 17 (9%) 167 0.486
(1.00) 		0.621
(1.00) 		0.682
(1.00) 		0.118
(1.00) 		1
(1.00) 		0.00283
(1.00) 		0.938
(1.00) 		0.711
(1.00)
CDH9 29 (16%) 155 0.27
(1.00) 		0.329
(1.00) 		0.066
(1.00) 		1
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.142
(1.00) 		0.0607
(1.00)
HIST1H2AA 7 (4%) 177 0.675
(1.00) 		0.999
(1.00) 		0.556
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.93
(1.00) 		0.64
(1.00)
GFRAL 25 (14%) 159 0.941
(1.00) 		0.945
(1.00) 		0.155
(1.00) 		0.823
(1.00) 		0.356
(1.00) 		0.528
(1.00) 		0.158
(1.00) 		0.0611
(1.00)
TBC1D3B 4 (2%) 180 0.0276
(1.00) 		0.318
(1.00) 		0.27
(1.00) 		1
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.958
(1.00) 		0.666
(1.00)
HHLA2 13 (7%) 171 0.59
(1.00) 		0.205
(1.00) 		0.225
(1.00) 		0.773
(1.00) 		0.198
(1.00) 		0.958
(1.00) 		0.009
(1.00) 		0.887
(1.00)
COPG2 3 (2%) 181 0.424
(1.00) 		0.986
(1.00) 		0.816
(1.00) 		1
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.987
(1.00) 		0.0148
(1.00)
IL32 8 (4%) 176 0.0287
(1.00) 		0.764
(1.00) 		0.586
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.985
(1.00) 		0.878
(1.00) 		0.00296
(1.00)
PRB4 18 (10%) 166 0.0419
(1.00) 		0.143
(1.00) 		0.108
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.644
(1.00) 		0.0674
(1.00) 		0.776
(1.00)
NBPF7 9 (5%) 175 0.0292
(1.00) 		0.0335
(1.00) 		0.467
(1.00) 		0.16
(1.00) 		0.00625
(1.00) 		0.981
(1.00) 		0.00404
(1.00) 		0.772
(1.00)
POM121 12 (7%) 172 0.219
(1.00) 		0.968
(1.00) 		0.337
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.0261
(1.00) 		0.0167
(1.00)
ARID2 28 (15%) 156 0.79
(1.00) 		0.0461
(1.00) 		0.418
(1.00) 		0.284
(1.00) 		0.392
(1.00) 		0.856
(1.00) 		0.126
(1.00) 		0.251
(1.00)
MAP2K1 9 (5%) 175 0.774
(1.00) 		0.439
(1.00) 		0.0663
(1.00) 		1
(1.00) 		1
(1.00) 		0.0831
(1.00) 		0.288
(1.00) 		0.915
(1.00)
DEFB118 7 (4%) 177 0.0832
(1.00) 		0.612
(1.00) 		0.765
(1.00) 		1
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.0027
(1.00) 		0.641
(1.00)
HBD 9 (5%) 175 0.125
(1.00) 		0.885
(1.00) 		0.302
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.894
(1.00) 		0.25
(1.00)
GLRB 22 (12%) 162 0.53
(1.00) 		0.222
(1.00) 		0.0603
(1.00) 		0.814
(1.00) 		1
(1.00) 		0.766
(1.00) 		0.259
(1.00) 		0.93
(1.00)
NR1H4 12 (7%) 172 0.596
(1.00) 		0.629
(1.00) 		0.898
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.0128
(1.00) 		0.548
(1.00)
OR51S1 19 (10%) 165 0.595
(1.00) 		0.232
(1.00) 		0.876
(1.00) 		0.803
(1.00) 		0.28
(1.00) 		0.918
(1.00) 		0.0538
(1.00) 		0.322
(1.00)
TFEC 15 (8%) 169 0.316
(1.00) 		0.128
(1.00) 		0.656
(1.00) 		1
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.00122
(1.00) 		0.478
(1.00)
UNC119B 3 (2%) 181 0.956
(1.00) 		0.369
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.987
(1.00) 		0.441
(1.00)
ZNF479 18 (10%) 166 0.438
(1.00) 		0.129
(1.00) 		0.74
(1.00) 		1
(1.00) 		1
(1.00) 		0.383
(1.00) 		0.217
(1.00) 		0.853
(1.00)
FAM19A1 9 (5%) 175 0.346
(1.00) 		0.701
(1.00) 		0.665
(1.00) 		1
(1.00) 		0.14
(1.00) 		0.981
(1.00) 		0.529
(1.00) 		0.761
(1.00)
GIMAP7 13 (7%) 171 0.812
(1.00) 		0.0371
(1.00) 		0.83
(1.00) 		0.14
(1.00) 		0.198
(1.00) 		0.958
(1.00) 		0.519
(1.00) 		0.25
(1.00)
KLHL4 18 (10%) 166 0.114
(1.00) 		0.592
(1.00) 		0.371
(1.00) 		0.799
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.0813
(1.00) 		0.518
(1.00)
NOTCH2NL 9 (5%) 175 0.941
(1.00) 		0.801
(1.00) 		0.175
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.356
(1.00) 		0.319
(1.00)
PRC1 9 (5%) 175 0.72
(1.00) 		0.42
(1.00) 		0.608
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.775
(1.00) 		0.941
(1.00)
PDE1A 27 (15%) 157 0.83
(1.00) 		0.135
(1.00) 		0.103
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.832
(1.00) 		0.0725
(1.00) 		0.509
(1.00)
GML 9 (5%) 175 0.893
(1.00) 		0.0617
(1.00) 		1
(1.00) 		0.16
(1.00) 		0.14
(1.00) 		0.981
(1.00) 		0.529
(1.00) 		0.913
(1.00)
OR4N2 21 (11%) 163 0.86
(1.00) 		0.255
(1.00) 		0.891
(1.00) 		0.00709
(1.00) 		0.306
(1.00) 		0.0681
(1.00) 		0.192
(1.00) 		0.683
(1.00)
ACSM2B 33 (18%) 151 0.513
(1.00) 		0.832
(1.00) 		0.2
(1.00) 		0.00837
(1.00) 		0.449
(1.00) 		0.754
(1.00) 		0.14
(1.00) 		0.862
(1.00)
USP17L2 16 (9%) 168 0.936
(1.00) 		0.718
(1.00) 		0.638
(1.00) 		0.177
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.0758
(1.00) 		0.0453
(1.00)
TAF1A 10 (5%) 174 0.148
(1.00) 		0.54
(1.00) 		0.646
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.119
(1.00) 		0.802
(1.00) 		0.762
(1.00)
OR5H2 13 (7%) 171 0.231
(1.00) 		0.0145
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.951
(1.00) 		0.0178
(1.00) 		0.587
(1.00)
PHGDH 8 (4%) 176 0.852
(1.00) 		0.727
(1.00) 		0.558
(1.00) 		0.0521
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.000456
(0.379) 		0.0751
(1.00)
BAGE2 12 (7%) 172 0.519
(1.00) 		0.979
(1.00) 		0.12
(1.00) 		1
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.0377
(1.00) 		0.361
(1.00)
FUT9 18 (10%) 166 0.225
(1.00) 		0.0357
(1.00) 		0.409
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.0859
(1.00) 		0.201
(1.00)
MPP7 22 (12%) 162 0.876
(1.00) 		0.0158
(1.00) 		1
(1.00) 		0.237
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.114
(1.00) 		0.93
(1.00)
TRAT1 11 (6%) 173 0.0646
(1.00) 		0.582
(1.00) 		0.922
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.00975
(1.00) 		0.765
(1.00)
TUBB8 9 (5%) 175 0.891
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.493
(1.00) 		0.14
(1.00) 		0.985
(1.00) 		0.0022
(1.00) 		0.8
(1.00)
ACD 8 (4%) 176 0.837
(1.00) 		0.852
(1.00) 		0.205
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.00461
(1.00) 		0.418
(1.00)
C8A 23 (12%) 161 0.48
(1.00) 		0.0682
(1.00) 		1
(1.00) 		0.0623
(1.00) 		0.332
(1.00) 		0.0797
(1.00) 		0.345
(1.00) 		0.45
(1.00)
KIAA1257 8 (4%) 176 0.259
(1.00) 		0.343
(1.00) 		0.682
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.919
(1.00) 		0.766
(1.00)
SNAP91 22 (12%) 162 0.634
(1.00) 		0.184
(1.00) 		0.507
(1.00) 		0.0956
(1.00) 		1
(1.00) 		0.489
(1.00) 		0.258
(1.00) 		0.931
(1.00)
CCK 5 (3%) 179 0.102
(1.00) 		0.756
(1.00) 		0.73
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.00752
(1.00) 		0.7
(1.00)
ANXA10 11 (6%) 173 0.375
(1.00) 		0.832
(1.00) 		0.828
(1.00) 		0.332
(1.00) 		0.00948
(1.00) 		0.976
(1.00) 		0.01
(1.00) 		0.627
(1.00)
LIN7A 9 (5%) 175 0.725
(1.00) 		0.61
(1.00) 		0.302
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.00212
(1.00) 		0.428
(1.00)
C2 8 (4%) 176 0.824
(1.00) 		0.678
(1.00) 		0.796
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.000522
(0.434) 		0.262
(1.00)
DGAT2L6 10 (5%) 174 0.331
(1.00) 		0.37
(1.00) 		0.405
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.00413
(1.00) 		0.705
(1.00)
OR2L3 15 (8%) 169 0.901
(1.00) 		0.895
(1.00) 		0.139
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.0202
(1.00) 		0.0695
(1.00) 		0.235
(1.00)
ZNF679 16 (9%) 168 0.96
(1.00) 		0.279
(1.00) 		0.78
(1.00) 		1
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.794
(1.00) 		0.264
(1.00)
NAP1L4 7 (4%) 177 0.207
(1.00) 		0.171
(1.00) 		0.817
(1.00) 		0.703
(1.00) 		0.11
(1.00) 		0.985
(1.00) 		0.386
(1.00) 		0.395
(1.00)
PARM1 14 (8%) 170 0.36
(1.00) 		0.261
(1.00) 		0.243
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.951
(1.00) 		0.000642
(0.533) 		0.11
(1.00)
DEFB119 6 (3%) 178 0.237
(1.00) 		0.174
(1.00) 		0.214
(1.00) 		1
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.953
(1.00) 		0.362
(1.00)
RGS18 8 (4%) 176 0.839
(1.00) 		0.239
(1.00) 		0.39
(1.00) 		0.0521
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.948
(1.00) 		0.889
(1.00)
VEGFC 16 (9%) 168 0.944
(1.00) 		0.849
(1.00) 		0.208
(1.00) 		0.587
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.0113
(1.00) 		0.185
(1.00)
ARL16 5 (3%) 179 0.191
(1.00) 		0.0305
(1.00) 		0.0513
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.853
(1.00) 		0.0868
(1.00)
CACNA1H 20 (11%) 164 0.41
(1.00) 		0.689
(1.00) 		0.945
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.918
(1.00) 		0.169
(1.00) 		0.507
(1.00)
CCNE2 10 (5%) 174 0.0495
(1.00) 		0.915
(1.00) 		0.0701
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.896
(1.00) 		0.326
(1.00)
FRG2B 11 (6%) 173 0.732
(1.00) 		0.0269
(1.00) 		0.958
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.859
(1.00) 		0.581
(1.00)
SPAG16 14 (8%) 170 0.597
(1.00) 		0.437
(1.00) 		0.943
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.958
(1.00) 		0.0382
(1.00) 		0.373
(1.00)
USP29 30 (16%) 154 0.238
(1.00) 		0.0293
(1.00) 		0.721
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.82
(1.00) 		0.206
(1.00) 		0.15
(1.00)
GH2 10 (5%) 174 0.482
(1.00) 		0.517
(1.00) 		0.391
(1.00) 		1
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.00166
(1.00) 		0.0335
(1.00)
ST18 36 (20%) 148 0.847
(1.00) 		0.173
(1.00) 		0.743
(1.00) 		1
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.353
(1.00) 		0.273
(1.00)
CCDC102B 21 (11%) 163 0.448
(1.00) 		0.502
(1.00) 		0.891
(1.00) 		1
(1.00) 		1
(1.00) 		0.899
(1.00) 		0.0766
(1.00) 		0.834
(1.00)
B2M 4 (2%) 180 0.535
(1.00) 		0.383
(1.00) 		0.862
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.987
(1.00) 		0.595
(1.00)
CD2 15 (8%) 169 0.328
(1.00) 		0.291
(1.00) 		0.36
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.0477
(1.00) 		0.0983
(1.00) 		0.658
(1.00)
SLC38A4 24 (13%) 160 0.982
(1.00) 		0.12
(1.00) 		0.39
(1.00) 		0.0405
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.304
(1.00) 		0.963
(1.00)
OR8D4 9 (5%) 175 0.0307
(1.00) 		0.656
(1.00) 		0.394
(1.00) 		1
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.0051
(1.00) 		0.934
(1.00)
MKX 11 (6%) 173 0.319
(1.00) 		0.719
(1.00) 		0.679
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.00501
(1.00) 		0.0131
(1.00)
SPATA8 8 (4%) 176 0.702
(1.00) 		0.0348
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.00243
(1.00) 		0.312
(1.00)
GPR137 8 (4%) 176 0.0484
(1.00) 		0.965
(1.00) 		0.648
(1.00) 		0.0521
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.0022
(1.00) 		0.856
(1.00)
GRXCR2 12 (7%) 172 0.229
(1.00) 		0.906
(1.00) 		0.577
(1.00) 		1
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.0145
(1.00) 		0.578
(1.00)
C2ORF40 4 (2%) 180 0.891
(1.00) 		0.422
(1.00) 		0.0647
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.958
(1.00)
CADM2 18 (10%) 166 0.349
(1.00) 		0.999
(1.00) 		0.361
(1.00) 		1
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.0626
(1.00) 		0.494
(1.00)
OR5J2 11 (6%) 173 0.605
(1.00) 		0.805
(1.00) 		0.543
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.994
(1.00) 		0.715
(1.00)
SIGLEC14 8 (4%) 176 0.652
(1.00) 		0.0468
(1.00) 		0.164
(1.00) 		0.0521
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.0027
(1.00) 		0.267
(1.00)
CX3CL1 3 (2%) 181 0.408
(1.00) 		0.925
(1.00) 		0.635
(1.00) 		1
(1.00) 		1
(1.00)
OR52J3 12 (7%) 172 0.215
(1.00) 		0.296
(1.00) 		0.611
(1.00) 		1
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.0213
(1.00) 		0.752
(1.00)
RUNDC3B 13 (7%) 171 0.692
(1.00) 		0.111
(1.00) 		0.855
(1.00) 		0.14
(1.00) 		0.198
(1.00) 		0.964
(1.00) 		0.057
(1.00) 		0.913
(1.00)
'OXA1L MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 1.73e-05 (Chi-square test), Q value = 0.014

Table S1.  Gene #5: 'OXA1L MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
OXA1L MUTATED 2 0 1 1 1 0 0 0 0 0
OXA1L WILD-TYPE 96 2 7 14 0 5 13 6 18 4

Figure S1.  Get High-res Image Gene #5: 'OXA1L MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'MUC7 MUTATION STATUS' versus 'AGE'

P value = 0.000286 (t-test), Q value = 0.24

Table S2.  Gene #20: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 181 56.6 (15.7)
MUC7 MUTATED 11 72.7 (10.9)
MUC7 WILD-TYPE 170 55.5 (15.4)

Figure S2.  Get High-res Image Gene #20: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'

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

P value = 1.35e-06 (Chi-square test), Q value = 0.0011

Table S3.  Gene #36: 'ANKRD20A4 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
ANKRD20A4 MUTATED 2 0 0 1 1 0 0 0 0 0
ANKRD20A4 WILD-TYPE 96 2 8 14 0 5 13 6 18 4

Figure S3.  Get High-res Image Gene #36: 'ANKRD20A4 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'ZMAT4 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 8.12e-06 (Chi-square test), Q value = 0.0068

Table S4.  Gene #48: 'ZMAT4 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
ZMAT4 MUTATED 2 0 0 0 1 0 1 1 0 0
ZMAT4 WILD-TYPE 96 2 8 15 0 5 12 5 18 4

Figure S4.  Get High-res Image Gene #48: 'ZMAT4 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 5.79e-06 (Chi-square test), Q value = 0.0049

Table S5.  Gene #61: 'C9ORF119 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
C9ORF119 MUTATED 2 0 0 2 1 0 0 0 0 0
C9ORF119 WILD-TYPE 96 2 8 13 0 5 13 6 18 4

Figure S5.  Get High-res Image Gene #61: 'C9ORF119 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 3.33e-06 (Chi-square test), Q value = 0.0028

Table S6.  Gene #68: 'SPINK13 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
SPINK13 MUTATED 2 0 0 3 1 0 0 0 0 0
SPINK13 WILD-TYPE 96 2 8 12 0 5 13 6 18 4

Figure S6.  Get High-res Image Gene #68: 'SPINK13 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 5.24e-05 (Chi-square test), Q value = 0.044

Table S7.  Gene #73: 'RAPGEF5 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
RAPGEF5 MUTATED 2 0 1 2 1 0 0 0 0 1
RAPGEF5 WILD-TYPE 96 2 7 13 0 5 13 6 18 3

Figure S7.  Get High-res Image Gene #73: 'RAPGEF5 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 1.55e-10 (Chi-square test), Q value = 1.3e-07

Table S8.  Gene #103: 'GNAI2 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
GNAI2 MUTATED 1 0 0 0 1 0 0 1 0 0
GNAI2 WILD-TYPE 97 2 8 15 0 5 13 5 18 4

Figure S8.  Get High-res Image Gene #103: 'GNAI2 MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

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

P value = 5.86e-05 (Chi-square test), Q value = 0.049

Table S9.  Gene #105: 'AREG MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
ALL 98 2 8 15 1 5 13 6 18 4
AREG MUTATED 3 0 0 0 1 0 0 0 1 0
AREG WILD-TYPE 95 2 8 15 0 5 13 6 17 4

Figure S9.  Get High-res Image Gene #105: 'AREG MUTATION STATUS' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

Methods & Data
Input

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

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

  • Number of patients = 184

  • Number of significantly mutated genes = 106

  • Number of selected clinical features = 9

  • 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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