Skin Cutaneous Melanoma: Correlation between gene mutation status and selected clinical features
(All_Samples cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] 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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