This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 2 genes and 37 clinical features across 37 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 |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED |
NUMBER OF LYMPH NODES |
RACE |
WEIGHT KG AT DIAGNOSIS |
TUMOR STATUS |
NEOPLASMHISTOLOGICGRADE |
TOBACCO SMOKING YEAR STOPPED |
TOBACCO SMOKING PACK YEARS SMOKED |
TOBACCO SMOKING HISTORY |
PATIENT AGEBEGANSMOKINGINYEARS |
RADIATION THERAPY TYPE |
PREGNANCIES COUNT TOTAL |
PREGNANCIES COUNT STILLBIRTH |
PATIENT PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT |
PREGNANCIES COUNT LIVE BIRTH |
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT |
PREGNANCIES COUNT ECTOPIC |
LOCATION OF POSITIVE MARGINS |
MENOPAUSE STATUS |
LYMPHOVASCULAR INVOLVEMENT |
LYMPH NODES EXAMINED HE COUNT |
LYMPH NODES EXAMINED |
KERATINIZATION SQUAMOUS CELL |
INITIAL PATHOLOGIC DX YEAR |
HISTORY HORMONAL CONTRACEPTIVES USE |
HEIGHT CM AT DIAGNOSIS |
CORPUS INVOLVEMENT |
CERVIX SUV RESULTS |
AJCC TUMOR PATHOLOGIC PT |
AGE AT DIAGNOSIS |
||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | |
NFE2L2 | 6 (16%) | 31 |
0.883 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.0318 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.68 (1.00) |
1 (1.00) |
0.426 (1.00) |
0.636 (1.00) |
0.466 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.183 (1.00) |
0.454 (1.00) |
0.566 (1.00) |
0.281 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.344 (1.00) |
0.824 (1.00) |
0.287 (1.00) |
0.426 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.577 (1.00) |
0.628 (1.00) |
0.725 (1.00) |
1 (1.00) |
1 (1.00) |
0.621 (1.00) |
|||
PIK3CA | 8 (22%) | 29 |
0.261 (1.00) |
0.0322 (1.00) |
0.603 (1.00) |
0.0671 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.423 (1.00) |
0.875 (1.00) |
0.283 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.0274 (1.00) |
0.811 (1.00) |
0.875 (1.00) |
0.116 (1.00) |
0.55 (1.00) |
0.391 (1.00) |
0.618 (1.00) |
0.367 (1.00) |
0.129 (1.00) |
0.763 (1.00) |
0.557 (1.00) |
0.343 (1.00) |
0.156 (1.00) |
0.286 (1.00) |
0.283 (1.00) |
0.0208 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.211 (1.00) |
0.218 (1.00) |
0.0278 (1.00) |
0.399 (1.00) |
0.0322 (1.00) |
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Mutation data file = transformed.cor.cli.txt
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Clinical data file = CESC-TP.merged_data.txt
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Number of patients = 37
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Number of significantly mutated genes = 2
-
Number of selected clinical features = 37
-
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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.