This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 48 genes and 7 clinical features across 327 patients, no significant finding detected with Q value < 0.25.
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No gene mutations related to clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) | ||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
VHL | 99 (30%) | 228 |
0.536 (1.00) |
0.124 (1.00) |
0.802 (1.00) |
0.779 (1.00) |
0.331 (1.00) |
0.624 (1.00) |
|
SETD2 | 25 (8%) | 302 |
0.788 (1.00) |
0.205 (1.00) |
0.516 (1.00) |
0.169 (1.00) |
1 (1.00) |
0.569 (1.00) |
|
PBRM1 | 78 (24%) | 249 |
0.434 (1.00) |
0.92 (1.00) |
0.282 (1.00) |
0.549 (1.00) |
0.354 (1.00) |
0.721 (1.00) |
0.479 (1.00) |
BAP1 | 20 (6%) | 307 |
0.0342 (1.00) |
0.784 (1.00) |
0.0028 (0.806) |
0.0705 (1.00) |
0.315 (1.00) |
0.106 (1.00) |
|
KDM5C | 16 (5%) | 311 |
0.0216 (1.00) |
0.0481 (1.00) |
0.0135 (1.00) |
0.833 (1.00) |
0.474 (1.00) |
0.727 (1.00) |
|
KRTAP5-5 | 8 (2%) | 319 |
0.261 (1.00) |
0.405 (1.00) |
0.267 (1.00) |
0.398 (1.00) |
1 (1.00) |
0.364 (1.00) |
|
PTEN | 11 (3%) | 316 |
0.545 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.803 (1.00) |
0.272 (1.00) |
1 (1.00) |
|
TP53 | 9 (3%) | 318 |
0.203 (1.00) |
0.313 (1.00) |
1 (1.00) |
0.0775 (1.00) |
0.328 (1.00) |
0.639 (1.00) |
|
MUC4 | 12 (4%) | 315 |
0.196 (1.00) |
0.342 (1.00) |
0.762 (1.00) |
0.196 (1.00) |
1 (1.00) |
0.699 (1.00) |
|
KANK3 | 5 (2%) | 322 |
0.962 (1.00) |
0.479 (1.00) |
1 (1.00) |
0.2 (1.00) |
1 (1.00) |
1 (1.00) |
|
POLDIP2 | 4 (1%) | 323 |
0.388 (1.00) |
0.129 (1.00) |
1 (1.00) |
0.648 (1.00) |
1 (1.00) |
0.502 (1.00) |
|
NF1 | 13 (4%) | 314 |
0.565 (1.00) |
0.275 (1.00) |
0.776 (1.00) |
0.24 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.235 (1.00) |
TSPAN19 | 4 (1%) | 323 |
0.583 (1.00) |
0.414 (1.00) |
1 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.502 (1.00) |
|
PTPN18 | 5 (2%) | 322 |
0.617 (1.00) |
0.251 (1.00) |
0.657 (1.00) |
0.587 (1.00) |
1 (1.00) |
0.582 (1.00) |
|
KRTAP4-1 | 3 (1%) | 324 |
0.646 (1.00) |
0.186 (1.00) |
0.0462 (1.00) |
0.75 (1.00) |
1 (1.00) |
1 (1.00) |
|
FAM200A | 5 (2%) | 322 |
0.341 (1.00) |
0.886 (1.00) |
0.0589 (1.00) |
0.491 (1.00) |
1 (1.00) |
1 (1.00) |
|
CD300E | 4 (1%) | 323 |
0.492 (1.00) |
0.811 (1.00) |
0.622 (1.00) |
0.204 (1.00) |
1 (1.00) |
1 (1.00) |
|
LGALS9B | 3 (1%) | 324 |
0.328 (1.00) |
0.811 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
PIK3CA | 8 (2%) | 319 |
0.732 (1.00) |
0.987 (1.00) |
0.466 (1.00) |
0.254 (1.00) |
0.429 (1.00) |
1 (1.00) |
|
CRIPAK | 3 (1%) | 324 |
0.409 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.0544 (1.00) |
1 (1.00) |
1 (1.00) |
|
FMN2 | 7 (2%) | 320 |
0.29 (1.00) |
0.544 (1.00) |
1 (1.00) |
0.701 (1.00) |
1 (1.00) |
1 (1.00) |
|
NAT8 | 3 (1%) | 324 |
0.707 (1.00) |
0.34 (1.00) |
1 (1.00) |
0.392 (1.00) |
1 (1.00) |
||
NDUFA13 | 3 (1%) | 324 |
0.407 (1.00) |
0.847 (1.00) |
0.556 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.406 (1.00) |
|
ADAMTS20 | 8 (2%) | 319 |
0.189 (1.00) |
0.282 (1.00) |
0.466 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.118 (1.00) |
|
STAG2 | 7 (2%) | 320 |
0.681 (1.00) |
0.026 (1.00) |
1 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.602 (1.00) |
|
KRT1 | 4 (1%) | 323 |
0.12 (1.00) |
0.121 (1.00) |
0.622 (1.00) |
0.521 (1.00) |
1 (1.00) |
1 (1.00) |
|
JMJD6 | 4 (1%) | 323 |
0.262 (1.00) |
0.141 (1.00) |
1 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.502 (1.00) |
|
NF2 | 4 (1%) | 323 |
0.889 (1.00) |
0.00795 (1.00) |
0.136 (1.00) |
0.405 (1.00) |
0.146 (1.00) |
0.502 (1.00) |
|
RECQL5 | 4 (1%) | 323 |
0.465 (1.00) |
0.294 (1.00) |
0.136 (1.00) |
0.648 (1.00) |
1 (1.00) |
1 (1.00) |
|
TGM5 | 5 (2%) | 322 |
0.389 (1.00) |
0.314 (1.00) |
0.00579 (1.00) |
0.491 (1.00) |
0.146 (1.00) |
0.582 (1.00) |
|
LHFPL1 | 3 (1%) | 324 |
0.492 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.75 (1.00) |
1 (1.00) |
1 (1.00) |
|
ZNF800 | 5 (2%) | 322 |
0.619 (1.00) |
0.467 (1.00) |
0.657 (1.00) |
1 (1.00) |
1 (1.00) |
0.582 (1.00) |
|
MCPH1 | 5 (2%) | 322 |
0.586 (1.00) |
0.609 (1.00) |
0.164 (1.00) |
0.848 (1.00) |
1 (1.00) |
0.181 (1.00) |
|
NKAIN3 | 3 (1%) | 324 |
0.954 (1.00) |
0.00859 (1.00) |
1 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.406 (1.00) |
|
NOTCH1 | 6 (2%) | 321 |
0.673 (1.00) |
0.133 (1.00) |
0.091 (1.00) |
0.878 (1.00) |
0.146 (1.00) |
0.244 (1.00) |
|
PIK3CG | 4 (1%) | 323 |
0.934 (1.00) |
0.794 (1.00) |
1 (1.00) |
0.405 (1.00) |
1 (1.00) |
1 (1.00) |
|
SMAD4 | 4 (1%) | 323 |
0.983 (1.00) |
0.19 (1.00) |
0.622 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
ZDHHC1 | 3 (1%) | 324 |
0.244 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.53 (1.00) |
1 (1.00) |
1 (1.00) |
|
EME1 | 4 (1%) | 323 |
0.784 (1.00) |
0.0628 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
MUC16 | 24 (7%) | 303 |
0.43 (1.00) |
0.0774 (1.00) |
1 (1.00) |
0.106 (1.00) |
1 (1.00) |
1 (1.00) |
|
TPTE2 | 4 (1%) | 323 |
0.862 (1.00) |
0.88 (1.00) |
1 (1.00) |
0.246 (1.00) |
1 (1.00) |
1 (1.00) |
|
GPM6A | 3 (1%) | 324 |
0.244 (1.00) |
0.754 (1.00) |
1 (1.00) |
0.156 (1.00) |
0.146 (1.00) |
0.406 (1.00) |
|
CNOT1 | 7 (2%) | 320 |
0.0311 (1.00) |
0.661 (1.00) |
0.258 (1.00) |
0.27 (1.00) |
0.272 (1.00) |
0.308 (1.00) |
|
GPR174 | 3 (1%) | 324 |
0.912 (1.00) |
0.458 (1.00) |
0.296 (1.00) |
0.53 (1.00) |
0.146 (1.00) |
0.067 (1.00) |
|
GRID2 | 5 (2%) | 322 |
0.224 (1.00) |
0.0062 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
NFE2L2 | 4 (1%) | 323 |
0.894 (1.00) |
0.65 (1.00) |
0.622 (1.00) |
0.648 (1.00) |
1 (1.00) |
1 (1.00) |
|
DUOX1 | 6 (2%) | 321 |
0.798 (1.00) |
0.481 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
GPX3 | 3 (1%) | 324 |
0.42 (1.00) |
0.308 (1.00) |
0.296 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.406 (1.00) |
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Mutation data file = KIRC.mutsig.cluster.txt
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Clinical data file = KIRC.clin.merged.picked.txt
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Number of patients = 327
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Number of significantly mutated genes = 48
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Number of selected clinical features = 7
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Exclude genes that fewer than K tumors have mutations, K = 3
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
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
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
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.
This is an experimental feature. Location of data archives could not be determined.