Correlation between gene mutation status and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C19C6VH0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C19C6VH0
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.

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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