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 87 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'.

  • NMNAT3 mutation correlated to 'LYMPH.NODE.METASTASIS'.

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

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

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

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

  • TUBAL3 mutation correlated to 'LYMPH.NODE.METASTASIS'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 87 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
(0.0711) 		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
(0.165) 		0.835
(1.00) 		0.0325
(1.00)
NMNAT3 5 (3%) 156 0.933
(1.00) 		0.545
(1.00) 		0.0478
(1.00) 		1
(1.00) 		0.995
(1.00) 		2.89e-12
(1.73e-09) 		0.12
(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
(0.165) 		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
(0.00966) 		0.564
(1.00)
TSHB 4 (2%) 157 0.471
(1.00) 		0.95
(1.00) 		0.0305
(1.00) 		1
(1.00) 		0.995
(1.00) 		1.94e-06
(0.00116) 		0.319
(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
(0.0351) 		0.817
(1.00)
TUBAL3 8 (5%) 153 0.811
(1.00) 		0.632
(1.00) 		0.388
(1.00) 		0.711
(1.00) 		0.992
(1.00) 		2.59e-05
(0.0154) 		0.621
(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
(0.102) 		0.349
(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)
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)
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)
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)
DSG1 26 (16%) 135 0.0907
(1.00) 		0.956
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.838
(1.00) 		0.254
(1.00) 		0.422
(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)
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)
AOAH 17 (11%) 144 0.695
(1.00) 		0.1
(1.00) 		0.0108
(1.00) 		0.791
(1.00) 		0.362
(1.00) 		0.0219
(1.00) 		0.735
(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)
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)
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)
PPIAL4G 11 (7%) 150 0.0917
(1.00) 		0.0373
(1.00) 		0.741
(1.00) 		0.331
(1.00) 		0.97
(1.00) 		0.0327
(1.00) 		0.97
(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)
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)
THEMIS 16 (10%) 145 0.717
(1.00) 		0.409
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.223
(1.00) 		0.619
(1.00)
LRTM1 16 (10%) 145 0.886
(1.00) 		0.654
(1.00) 		0.712
(1.00) 		0.0527
(1.00) 		0.0381
(1.00) 		0.186
(1.00) 		0.611
(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)
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)
GPR141 12 (7%) 149 0.61
(1.00) 		0.993
(1.00) 		0.308
(1.00) 		0.538
(1.00) 		0.957
(1.00) 		0.057
(1.00) 		0.288
(1.00)
EIF2B1 8 (5%) 153 0.782
(1.00) 		0.772
(1.00) 		0.0838
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.938
(1.00) 		0.975
(1.00)
CHGB 18 (11%) 143 0.128
(1.00) 		0.918
(1.00) 		0.519
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.154
(1.00) 		0.173
(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)
MS4A2 8 (5%) 153 0.58
(1.00) 		0.528
(1.00) 		0.136
(1.00) 		0.26
(1.00) 		0.985
(1.00) 		0.0094
(1.00) 		0.867
(1.00)
MPP7 19 (12%) 142 0.992
(1.00) 		0.023
(1.00) 		0.891
(1.00) 		0.448
(1.00) 		0.471
(1.00) 		0.0976
(1.00) 		0.935
(1.00)
C1QTNF9 10 (6%) 151 0.176
(1.00) 		0.636
(1.00) 		0.0664
(1.00) 		0.328
(1.00) 		0.97
(1.00) 		0.902
(1.00) 		0.702
(1.00)
DNAH7 60 (37%) 101 0.414
(1.00) 		0.073
(1.00) 		0.552
(1.00) 		0.128
(1.00) 		0.247
(1.00) 		0.28
(1.00) 		0.939
(1.00)
FAM58A 3 (2%) 158 0.467
(1.00) 		0.41
(1.00) 		0.725
(1.00) 		0.299
(1.00) 		0.997
(1.00) 		0.41
(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)
SCN5A 40 (25%) 121 0.635
(1.00) 		0.199
(1.00) 		0.451
(1.00) 		0.575
(1.00) 		0.267
(1.00) 		0.481
(1.00) 		0.439
(1.00)
C6ORF223 3 (2%) 158 0.661
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.299
(1.00) 		0.997
(1.00) 		0.697
(1.00) 		0.341
(1.00)
LOC649330 20 (12%) 141 0.444
(1.00) 		0.031
(1.00) 		0.643
(1.00) 		0.324
(1.00) 		0.916
(1.00) 		0.235
(1.00) 		0.604
(1.00)
KLRC3 4 (2%) 157 0.471
(1.00) 		0.683
(1.00) 		0.778
(1.00) 		0.624
(1.00) 		0.995
(1.00) 		0.379
(1.00) 		0.848
(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)
PENK 15 (9%) 146 0.723
(1.00) 		0.611
(1.00) 		0.0764
(1.00) 		0.575
(1.00) 		0.95
(1.00) 		0.106
(1.00) 		0.372
(1.00)
OR4E2 16 (10%) 145 0.131
(1.00) 		0.587
(1.00) 		0.394
(1.00) 		0.416
(1.00) 		0.402
(1.00) 		0.144
(1.00) 		0.556
(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)
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)
PCDP1 12 (7%) 149 0.364
(1.00) 		0.58
(1.00) 		0.688
(1.00) 		0.538
(1.00) 		0.97
(1.00) 		0.0327
(1.00) 		0.148
(1.00)
ZFP106 6 (4%) 155 0.524
(1.00) 		0.000615
(0.363) 		0.491
(1.00) 		0.0864
(1.00) 		0.989
(1.00) 		0.81
(1.00) 		0.382
(1.00)
TCHHL1 25 (16%) 136 0.774
(1.00) 		0.031
(1.00) 		0.192
(1.00) 		0.658
(1.00) 		0.15
(1.00) 		0.207
(1.00) 		0.106
(1.00)
OR2W1 13 (8%) 148 0.546
(1.00) 		0.0459
(1.00) 		0.848
(1.00) 		0.551
(1.00) 		0.957
(1.00) 		0.0116
(1.00) 		0.931
(1.00)
LRRC4C 25 (16%) 136 0.359
(1.00) 		0.0553
(1.00) 		0.161
(1.00) 		0.658
(1.00) 		0.862
(1.00) 		0.421
(1.00) 		0.928
(1.00)
SERPINB10 7 (4%) 154 0.437
(1.00) 		0.327
(1.00) 		0.236
(1.00) 		0.424
(1.00) 		0.989
(1.00) 		0.00245
(1.00) 		0.845
(1.00)
C18ORF26 13 (8%) 148 0.608
(1.00) 		0.61
(1.00) 		0.0387
(1.00) 		0.135
(1.00) 		0.964
(1.00) 		0.0668
(1.00) 		0.872
(1.00)
TBC1D3B 3 (2%) 158 0.00198
(1.00) 		0.404
(1.00) 		0.285
(1.00) 		1
(1.00)
CCNE2 10 (6%) 151 0.0324
(1.00) 		0.879
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.946
(1.00) 		0.476
(1.00)
CAPZA3 13 (8%) 148 0.859
(1.00) 		0.0973
(1.00) 		0.515
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.114
(1.00) 		0.782
(1.00)
PROL1 15 (9%) 146 0.907
(1.00) 		0.224
(1.00) 		0.169
(1.00) 		0.26
(1.00) 		0.0277
(1.00) 		0.127
(1.00) 		0.807
(1.00)
CYP4X1 12 (7%) 149 0.552
(1.00) 		0.543
(1.00) 		0.834
(1.00) 		0.76
(1.00) 		0.964
(1.00) 		0.0173
(1.00) 		0.924
(1.00)
GCOM1 17 (11%) 144 0.363
(1.00) 		0.165
(1.00) 		0.25
(1.00) 		0.602
(1.00) 		0.438
(1.00) 		0.255
(1.00) 		0.135
(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)
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)
B2M 4 (2%) 157 0.577
(1.00) 		0.401
(1.00) 		0.778
(1.00) 		0.297
(1.00) 		0.997
(1.00) 		0.99
(1.00) 		0.655
(1.00)
KCNB2 43 (27%) 118 0.716
(1.00) 		0.533
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.144
(1.00) 		0.106
(1.00)
KIAA2022 31 (19%) 130 0.514
(1.00) 		0.0144
(1.00) 		0.272
(1.00) 		0.409
(1.00) 		0.813
(1.00) 		0.122
(1.00) 		0.349
(1.00)
KIAA1486 19 (12%) 142 0.332
(1.00) 		0.0274
(1.00) 		0.116
(1.00) 		0.0733
(1.00) 		0.438
(1.00) 		0.233
(1.00) 		0.701
(1.00)
APCS 9 (6%) 152 0.722
(1.00) 		0.291
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.0895
(1.00) 		0.00511
(1.00) 		0.393
(1.00)
SIRPB1 15 (9%) 146 0.841
(1.00) 		0.128
(1.00) 		0.241
(1.00) 		0.26
(1.00) 		0.95
(1.00) 		0.00318
(1.00) 		0.524
(1.00)
CYP7B1 14 (9%) 147 0.716
(1.00) 		0.733
(1.00) 		0.732
(1.00) 		0.259
(1.00) 		0.957
(1.00) 		0.111
(1.00) 		0.935
(1.00)
SGCZ 19 (12%) 142 0.243
(1.00) 		0.897
(1.00) 		0.945
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.0482
(1.00) 		0.183
(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)
CYP4Z1 13 (8%) 148 0.192
(1.00) 		0.239
(1.00) 		1
(1.00) 		1
(1.00) 		0.274
(1.00) 		0.0659
(1.00) 		0.684
(1.00)
FAM113B 16 (10%) 145 0.327
(1.00) 		0.278
(1.00) 		0.00353
(1.00) 		0.0527
(1.00) 		0.925
(1.00) 		0.169
(1.00) 		0.162
(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)
CX3CL1 3 (2%) 158 0.427
(1.00) 		0.938
(1.00) 		0.469
(1.00) 		1
(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)
IGF2BP3 3 (2%) 158 0.854
(1.00) 		0.687
(1.00) 		0.469
(1.00) 		1
(1.00)
SLC9A11 28 (17%) 133 0.766
(1.00) 		0.71
(1.00) 		0.732
(1.00) 		0.0845
(1.00) 		0.62
(1.00) 		0.422
(1.00) 		0.42
(1.00)
HRNR 37 (23%) 124 0.346
(1.00) 		0.39
(1.00) 		0.913
(1.00) 		0.0116
(1.00) 		0.674
(1.00) 		0.451
(1.00) 		0.602
(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)
TRHDE 33 (20%) 128 0.616
(1.00) 		0.138
(1.00) 		0.103
(1.00) 		0.231
(1.00) 		0.674
(1.00) 		0.325
(1.00) 		0.449
(1.00)
SPTLC3 15 (9%) 146 0.214
(1.00) 		0.546
(1.00) 		0.348
(1.00) 		0.575
(1.00) 		0.934
(1.00) 		0.119
(1.00) 		0.177
(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)
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)
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)
DNER 15 (9%) 146 0.479
(1.00) 		0.107
(1.00) 		0.485
(1.00) 		0.0536
(1.00) 		0.942
(1.00) 		0.212
(1.00) 		0.385
(1.00)
'OXA1L MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 0.00012 (Chi-square test), Q value = 0.071

Table S1.  Gene #5: '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 #5: '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 = 0.17

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'

'NMNAT3 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 2.89e-12 (Chi-square test), Q value = 1.7e-09

Table S3.  Gene #24: 'NMNAT3 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
NMNAT3 MUTATED 2 0 0 0 1 0 0 0 0 1
NMNAT3 WILD-TYPE 86 2 7 15 0 4 10 5 15 0

Figure S3.  Get High-res Image Gene #24: 'NMNAT3 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

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

P value = 0.000279 (Chi-square test), Q value = 0.17

Table S4.  Gene #28: '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 #28: '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 = 0.0097

Table S5.  Gene #37: '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 #37: 'ANKRD20A4 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

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

P value = 1.94e-06 (Chi-square test), Q value = 0.0012

Table S6.  Gene #43: 'TSHB 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
TSHB MUTATED 2 0 0 0 1 0 0 1 0 0
TSHB WILD-TYPE 86 2 7 15 0 4 10 4 15 1

Figure S6.  Get High-res Image Gene #43: 'TSHB 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 = 0.035

Table S7.  Gene #64: '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 S7.  Get High-res Image Gene #64: 'C9ORF119 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

'TUBAL3 MUTATION STATUS' versus 'LYMPH.NODE.METASTASIS'

P value = 2.59e-05 (Chi-square test), Q value = 0.015

Table S8.  Gene #65: 'TUBAL3 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
TUBAL3 MUTATED 1 0 0 2 1 0 1 0 0 0
TUBAL3 WILD-TYPE 87 2 7 13 0 4 9 5 15 1

Figure S8.  Get High-res Image Gene #65: 'TUBAL3 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 = 0.1

Table S9.  Gene #66: '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 S9.  Get High-res Image Gene #66: 'C2 MUTATION STATUS' versus Clinical Feature #6: 'LYMPH.NODE.METASTASIS'

Methods & Data
Input

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

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

  • Number of patients = 161

  • Number of significantly mutated genes = 87

  • 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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