This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 57 genes and 4 clinical features across 316 patients, no significant finding detected with Q value < 0.25.
-
No gene mutations related to clinical features.
Clinical Features |
Time to Death |
AGE |
KARNOFSKY PERFORMANCE SCORE |
NEOADJUVANT THERAPY |
||
nMutated (%) | nWild-Type | logrank test | t-test | t-test | Fisher's exact test | |
TP53 | 276 (87%) | 40 |
0.389 (1.00) |
0.649 (1.00) |
0.585 (1.00) |
0.505 (1.00) |
BRCA1 | 12 (4%) | 304 |
0.957 (1.00) |
0.65 (1.00) |
1 (1.00) |
|
RB1 | 9 (3%) | 307 |
0.241 (1.00) |
0.204 (1.00) |
0.658 (1.00) |
|
CSMD3 | 18 (6%) | 298 |
0.262 (1.00) |
0.61 (1.00) |
0.285 (1.00) |
0.53 (1.00) |
NF1 | 14 (4%) | 302 |
0.2 (1.00) |
0.606 (1.00) |
0.478 (1.00) |
|
FAT3 | 19 (6%) | 297 |
0.139 (1.00) |
0.743 (1.00) |
0.643 (1.00) |
0.215 (1.00) |
CYP11B1 | 7 (2%) | 309 |
0.0926 (1.00) |
0.793 (1.00) |
0.104 (1.00) |
|
CHST2 | 5 (2%) | 311 |
0.851 (1.00) |
0.0727 (1.00) |
1 (1.00) |
|
C9ORF171 | 5 (2%) | 311 |
0.895 (1.00) |
0.121 (1.00) |
0.746 (1.00) |
0.591 (1.00) |
DUSP19 | 4 (1%) | 312 |
0.785 (1.00) |
0.593 (1.00) |
0.536 (1.00) |
|
GABRA6 | 6 (2%) | 310 |
0.815 (1.00) |
0.0121 (1.00) |
0.595 (1.00) |
|
TACC3 | 5 (2%) | 311 |
0.0969 (1.00) |
0.626 (1.00) |
0.591 (1.00) |
|
CDK12 | 9 (3%) | 307 |
0.367 (1.00) |
0.214 (1.00) |
0.0171 (1.00) |
0.193 (1.00) |
EPHA7 | 7 (2%) | 309 |
0.309 (1.00) |
0.404 (1.00) |
0.61 (1.00) |
|
PPP1R3A | 8 (3%) | 308 |
0.539 (1.00) |
0.0819 (1.00) |
0.632 (1.00) |
|
USH2A | 20 (6%) | 296 |
0.338 (1.00) |
0.835 (1.00) |
0.0171 (1.00) |
0.761 (1.00) |
GLI2 | 9 (3%) | 307 |
0.133 (1.00) |
0.0829 (1.00) |
0.00971 (1.00) |
|
BRCA2 | 11 (3%) | 305 |
0.085 (1.00) |
0.372 (1.00) |
1 (1.00) |
|
FAM171B | 7 (2%) | 309 |
0.61 (1.00) |
0.388 (1.00) |
1 (1.00) |
|
ZNF479 | 5 (2%) | 311 |
0.539 (1.00) |
0.872 (1.00) |
1 (1.00) |
|
SI | 10 (3%) | 306 |
0.646 (1.00) |
0.219 (1.00) |
0.22 (1.00) |
|
C6ORF142 | 5 (2%) | 311 |
0.258 (1.00) |
0.147 (1.00) |
0.591 (1.00) |
|
SLCO1C1 | 6 (2%) | 310 |
0.741 (1.00) |
0.774 (1.00) |
0.595 (1.00) |
|
GAS2L1 | 4 (1%) | 312 |
0.178 (1.00) |
0.056 (1.00) |
0.141 (1.00) |
|
C1ORF95 | 3 (1%) | 313 |
0.72 (1.00) |
0.956 (1.00) |
1 (1.00) |
|
KCNJ12 | 5 (2%) | 311 |
0.688 (1.00) |
0.643 (1.00) |
0.591 (1.00) |
|
QSOX2 | 5 (2%) | 311 |
0.835 (1.00) |
0.8 (1.00) |
1 (1.00) |
|
TBP | 4 (1%) | 312 |
0.323 (1.00) |
0.191 (1.00) |
0.141 (1.00) |
|
ACBD4 | 3 (1%) | 313 |
0.811 (1.00) |
0.182 (1.00) |
1 (1.00) |
|
C10ORF113 | 3 (1%) | 313 |
0.0628 (1.00) |
0.83 (1.00) |
1 (1.00) |
|
GPR149 | 6 (2%) | 310 |
0.594 (1.00) |
0.166 (1.00) |
1 (1.00) |
|
PAOX | 4 (1%) | 312 |
0.446 (1.00) |
0.957 (1.00) |
0.536 (1.00) |
|
PXN | 5 (2%) | 311 |
0.238 (1.00) |
0.731 (1.00) |
1 (1.00) |
|
SNTG1 | 5 (2%) | 311 |
0.401 (1.00) |
0.417 (1.00) |
0.591 (1.00) |
|
EFEMP1 | 5 (2%) | 311 |
0.61 (1.00) |
0.0549 (1.00) |
0.591 (1.00) |
|
VN1R5 | 4 (1%) | 312 |
0.598 (1.00) |
0.805 (1.00) |
0.141 (1.00) |
|
MOGAT3 | 4 (1%) | 312 |
0.271 (1.00) |
0.905 (1.00) |
1 (1.00) |
|
TMEM132D | 7 (2%) | 309 |
0.343 (1.00) |
0.784 (1.00) |
0.734 (1.00) |
0.0193 (1.00) |
ARHGEF9 | 5 (2%) | 311 |
0.0717 (1.00) |
0.428 (1.00) |
1 (1.00) |
|
HIST1H1C | 4 (1%) | 312 |
0.0793 (1.00) |
0.888 (1.00) |
1 (1.00) |
|
TOP2A | 6 (2%) | 310 |
0.674 (1.00) |
0.0743 (1.00) |
0.0678 (1.00) |
|
ATP6AP1 | 4 (1%) | 312 |
0.699 (1.00) |
0.273 (1.00) |
1 (1.00) |
|
DEFB118 | 3 (1%) | 313 |
0.452 (1.00) |
0.216 (1.00) |
1 (1.00) |
|
HAS2 | 5 (2%) | 311 |
0.74 (1.00) |
0.19 (1.00) |
0.591 (1.00) |
|
LZTS2 | 4 (1%) | 312 |
0.0181 (1.00) |
0.189 (1.00) |
0.536 (1.00) |
|
PXDNL | 7 (2%) | 309 |
0.118 (1.00) |
0.433 (1.00) |
0.61 (1.00) |
|
RASAL1 | 6 (2%) | 310 |
0.991 (1.00) |
0.854 (1.00) |
0.281 (1.00) |
|
C10ORF140 | 5 (2%) | 311 |
0.916 (1.00) |
0.502 (1.00) |
1 (1.00) |
|
CLEC4F | 5 (2%) | 311 |
0.223 (1.00) |
0.622 (1.00) |
1 (1.00) |
|
GPX6 | 3 (1%) | 313 |
0.707 (1.00) |
0.68 (1.00) |
1 (1.00) |
|
KIT | 7 (2%) | 309 |
0.371 (1.00) |
0.0377 (1.00) |
0.61 (1.00) |
|
POTED | 4 (1%) | 312 |
0.184 (1.00) |
0.537 (1.00) |
0.536 (1.00) |
|
SDC1 | 4 (1%) | 312 |
0.71 (1.00) |
0.833 (1.00) |
1 (1.00) |
|
SON | 8 (3%) | 308 |
0.484 (1.00) |
0.0361 (1.00) |
1 (1.00) |
|
VSIG2 | 4 (1%) | 312 |
0.611 (1.00) |
0.787 (1.00) |
0.536 (1.00) |
|
PAX3 | 5 (2%) | 311 |
0.997 (1.00) |
0.949 (1.00) |
0.591 (1.00) |
|
SCEL | 5 (2%) | 311 |
0.795 (1.00) |
0.478 (1.00) |
1 (1.00) |
-
Mutation data file = OV.mutsig.cluster.txt
-
Clinical data file = OV.clin.merged.picked.txt
-
Number of patients = 316
-
Number of significantly mutated genes = 57
-
Number of selected clinical features = 4
-
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.