Skin Cutaneous Melanoma: Correlation between gene mutation status and selected clinical features
(All_Metastatic 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 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.

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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