Skin Cutaneous Melanoma: Correlation between gene mutation status and selected clinical features
(NF1_Any_Mutants 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 74 genes and 7 clinical features across 25 patients, no significant finding detected with Q value < 0.25.

  • No gene mutations related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 74 genes and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		GENDER 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 t-test Chi-square test
NRAS 8 (32%) 17 0.647
(1.00) 		0.577
(1.00) 		0.116
(1.00) 		1
(1.00) 		0.208
(1.00) 		0.71
(1.00)
TPTE 14 (56%) 11 0.107
(1.00) 		0.192
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.886
(1.00) 		0.466
(1.00)
TP53 7 (28%) 18 0.618
(1.00) 		0.389
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.209
(1.00) 		0.899
(1.00)
GRXCR1 7 (28%) 18 0.999
(1.00) 		0.511
(1.00) 		0.64
(1.00) 		0.528
(1.00) 		0.56
(1.00)
BRAF 7 (28%) 18 0.436
(1.00) 		0.145
(1.00) 		0.719
(1.00) 		0.64
(1.00) 		0.528
(1.00) 		0.441
(1.00)
TRAT1 7 (28%) 18 0.465
(1.00) 		0.553
(1.00) 		0.719
(1.00) 		0.64
(1.00) 		0.654
(1.00) 		0.496
(1.00)
ZNF585B 8 (32%) 17 0.187
(1.00) 		0.562
(1.00) 		0.00361
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.56
(1.00)
TPTE2 11 (44%) 14 0.5
(1.00) 		0.328
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.316
(1.00)
OR51S1 8 (32%) 17 0.763
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.17
(1.00)
RAC1 4 (16%) 21 0.264
(1.00) 		1
(1.00) 		0.57
(1.00) 		0.481
(1.00) 		0.587
(1.00)
CDKN2A 5 (20%) 20 0.899
(1.00) 		0.157
(1.00) 		0.657
(1.00) 		1
(1.00) 		1
(1.00) 		0.554
(1.00)
C7 11 (44%) 14 0.357
(1.00) 		0.401
(1.00) 		0.865
(1.00) 		0.081
(1.00) 		0.882
(1.00) 		0.719
(1.00)
C15ORF23 5 (20%) 20 0.836
(1.00) 		0.379
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.326
(1.00)
GLRB 6 (24%) 19 0.975
(1.00) 		0.585
(1.00) 		0.322
(1.00) 		0.344
(1.00) 		0.87
(1.00) 		0.483
(1.00)
FAM58A 3 (12%) 22 0.883
(1.00) 		0.565
(1.00) 		0.527
(1.00) 		0.481
(1.00)
EPHA6 11 (44%) 14 0.763
(1.00) 		0.449
(1.00) 		0.501
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.406
(1.00)
NAP1L2 7 (28%) 18 0.878
(1.00) 		0.417
(1.00) 		0.156
(1.00) 		1
(1.00) 		0.349
(1.00)
OR4K5 8 (32%) 17 0.528
(1.00) 		0.0785
(1.00) 		0.334
(1.00) 		1
(1.00) 		0.0443
(1.00) 		0.719
(1.00)
SLC9A11 11 (44%) 14 0.262
(1.00) 		0.954
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.349
(1.00)
ADAMTS20 15 (60%) 10 0.823
(1.00) 		0.32
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.2
(1.00) 		0.445
(1.00)
SLC38A4 9 (36%) 16 0.221
(1.00) 		0.526
(1.00) 		0.412
(1.00) 		0.182
(1.00) 		0.893
(1.00) 		0.406
(1.00)
OR2T2 5 (20%) 20 0.308
(1.00) 		0.344
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.912
(1.00)
PRB2 9 (36%) 16 0.896
(1.00) 		0.143
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.812
(1.00)
COL21A1 10 (40%) 15 0.00559
(1.00) 		0.929
(1.00) 		0.3
(1.00) 		0.0875
(1.00) 		0.882
(1.00) 		0.445
(1.00)
OR4N2 9 (36%) 16 0.48
(1.00) 		0.635
(1.00) 		0.547
(1.00) 		0.0218
(1.00) 		0.893
(1.00) 		0.609
(1.00)
PROX1 6 (24%) 19 0.899
(1.00) 		0.788
(1.00) 		0.265
(1.00) 		0.624
(1.00) 		0.263
(1.00) 		0.349
(1.00)
ANGPT1 9 (36%) 16 0.103
(1.00) 		0.823
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.562
(1.00) 		0.719
(1.00)
C8A 8 (32%) 17 0.738
(1.00) 		0.108
(1.00) 		0.0766
(1.00) 		0.205
(1.00) 		0.0707
(1.00) 		0.483
(1.00)
SERPINB11 7 (28%) 18 0.629
(1.00) 		0.56
(1.00) 		0.719
(1.00) 		1
(1.00) 		1
(1.00) 		0.39
(1.00)
C18ORF34 10 (40%) 15 0.927
(1.00) 		0.675
(1.00) 		0.424
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.854
(1.00)
FRG2B 5 (20%) 20 0.3
(1.00) 		0.544
(1.00) 		0.0235
(1.00) 		1
(1.00) 		0.554
(1.00)
LPPR1 4 (16%) 21 0.286
(1.00) 		0.796
(1.00) 		0.496
(1.00) 		0.269
(1.00) 		0.481
(1.00)
THEMIS 7 (28%) 18 0.649
(1.00) 		0.511
(1.00) 		0.64
(1.00) 		0.599
(1.00) 		0.854
(1.00)
SNAP91 7 (28%) 18 0.943
(1.00) 		0.329
(1.00) 		0.511
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.349
(1.00)
SLC27A6 8 (32%) 17 0.272
(1.00) 		0.0831
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.0923
(1.00)
CXORF22 8 (32%) 17 0.126
(1.00) 		0.499
(1.00) 		0.621
(1.00) 		0.359
(1.00) 		0.329
(1.00) 		0.805
(1.00)
NOBOX 8 (32%) 17 0.367
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.528
(1.00) 		0.512
(1.00)
MUC7 5 (20%) 20 0.0147
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.496
(1.00)
GIMAP7 5 (20%) 20 0.989
(1.00) 		0.821
(1.00) 		1
(1.00) 		1
(1.00) 		0.0455
(1.00) 		0.117
(1.00)
SYT17 5 (20%) 20 0.88
(1.00) 		0.285
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.554
(1.00)
ASB15 8 (32%) 17 0.125
(1.00) 		0.601
(1.00) 		1
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.198
(1.00)
OR4A15 6 (24%) 19 0.841
(1.00) 		0.0336
(1.00) 		0.322
(1.00) 		1
(1.00) 		0.0151
(1.00) 		0.738
(1.00)
PROL1 7 (28%) 18 0.813
(1.00) 		0.438
(1.00) 		0.719
(1.00) 		0.362
(1.00) 		0.297
(1.00) 		0.805
(1.00)
DSG3 13 (52%) 12 0.0195
(1.00) 		0.472
(1.00) 		0.0645
(1.00) 		0.673
(1.00) 		0.67
(1.00) 		0.126
(1.00)
OPRK1 9 (36%) 16 0.908
(1.00) 		0.691
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.533
(1.00) 		0.633
(1.00)
PCSK5 10 (40%) 15 0.695
(1.00) 		0.974
(1.00) 		0.862
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.466
(1.00)
OR52A1 6 (24%) 19 0.725
(1.00) 		0.908
(1.00) 		0.00903
(1.00) 		0.624
(1.00) 		0.0565
(1.00) 		0.614
(1.00)
ACSM2B 8 (32%) 17 0.62
(1.00) 		0.59
(1.00) 		0.241
(1.00) 		0.205
(1.00) 		0.562
(1.00) 		0.195
(1.00)
NOL4 11 (44%) 14 0.577
(1.00) 		0.472
(1.00) 		0.501
(1.00) 		0.234
(1.00) 		0.661
(1.00) 		0.727
(1.00)
PPFIA2 9 (36%) 16 0.669
(1.00) 		0.646
(1.00) 		0.745
(1.00) 		0.661
(1.00) 		0.0443
(1.00) 		0.0752
(1.00)
IL1F8 5 (20%) 20 0.539
(1.00) 		0.412
(1.00) 		0.0565
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.571
(1.00)
UGT2A1 6 (24%) 19 0.71
(1.00) 		0.0558
(1.00) 		0.138
(1.00) 		0.624
(1.00) 		0.142
(1.00) 		0.805
(1.00)
SYT13 3 (12%) 22 0.549
(1.00) 		0.152
(1.00) 		1
(1.00)
ASAH2 6 (24%) 19 0.306
(1.00) 		0.83
(1.00) 		0.624
(1.00) 		0.401
(1.00) 		0.349
(1.00)
ZNF679 7 (28%) 18 0.916
(1.00) 		0.844
(1.00) 		1
(1.00) 		1
(1.00) 		0.275
(1.00)
C10ORF54 4 (16%) 21 0.246
(1.00) 		0.393
(1.00) 		0.496
(1.00) 		0.269
(1.00) 		0.352
(1.00) 		0.236
(1.00)
C10ORF120 6 (24%) 19 0.267
(1.00) 		0.265
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.752
(1.00)
CHSY1 4 (16%) 21 0.955
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.167
(1.00)
CSF2RA 6 (24%) 19 0.772
(1.00) 		0.578
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.87
(1.00) 		0.095
(1.00)
KCND2 8 (32%) 17 0.961
(1.00) 		0.767
(1.00) 		0.445
(1.00) 		0.359
(1.00) 		0.263
(1.00) 		0.752
(1.00)
SPEF2 11 (44%) 14 0.707
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.796
(1.00) 		0.233
(1.00)
RPGRIP1 6 (24%) 19 0.551
(1.00) 		0.174
(1.00) 		0.129
(1.00) 		0.654
(1.00) 		0.243
(1.00)
OR2L3 3 (12%) 22 0.0735
(1.00) 		0.763
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.854
(1.00)
CCDC54 5 (20%) 20 0.967
(1.00) 		0.833
(1.00) 		0.347
(1.00) 		1
(1.00) 		1
(1.00)
KLHL14 5 (20%) 20 0.447
(1.00) 		0.942
(1.00) 		1
(1.00) 		1
(1.00) 		0.135
(1.00) 		0.854
(1.00)
ZFX 7 (28%) 18 0.635
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.528
(1.00) 		0.56
(1.00)
KLHL13 10 (40%) 15 0.909
(1.00) 		0.94
(1.00) 		1
(1.00) 		0.194
(1.00) 		0.893
(1.00) 		0.752
(1.00)
NSUN7 3 (12%) 22 0.414
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.854
(1.00)
VEGFC 6 (24%) 19 0.301
(1.00) 		0.322
(1.00) 		0.0593
(1.00) 		0.708
(1.00) 		0.496
(1.00)
TMEM202 5 (20%) 20 0.00698
(1.00) 		0.00211
(0.883) 		0.226
(1.00) 		0.283
(1.00) 		0.135
(1.00) 		0.438
(1.00)
ERC2 12 (48%) 13 0.076
(1.00) 		0.801
(1.00) 		0.0838
(1.00) 		0.0302
(1.00) 		0.167
(1.00) 		0.141
(1.00)
GRM3 10 (40%) 15 0.484
(1.00) 		0.932
(1.00) 		0.862
(1.00) 		0.402
(1.00) 		0.13
(1.00) 		0.138
(1.00)
CDH12 8 (32%) 17 0.406
(1.00) 		0.334
(1.00) 		0.359
(1.00) 		0.528
(1.00) 		0.081
(1.00)
SIRPB1 6 (24%) 19 0.632
(1.00) 		0.303
(1.00) 		0.174
(1.00) 		0.129
(1.00) 		0.708
(1.00) 		0.788
(1.00)
Methods & Data
Input

  • Mutation data file = SKCM-NF1_Any_Mutants.mutsig.cluster.txt

  • Clinical data file = SKCM-NF1_Any_Mutants.clin.merged.picked.txt

  • Number of patients = 25

  • Number of significantly mutated genes = 74

  • Number of selected clinical features = 7

  • 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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