This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17353 genes and 4 clinical features across 59 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.
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1 gene correlated to 'GENDER'.
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KIF4B
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No genes correlated to 'Time to Death', 'AGE', and 'KARNOFSKY.PERFORMANCE.SCORE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=1 | male | N=0 | female | N=1 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0.4-118.9 (median=8.2) |
censored | N = 39 | |
death | N = 20 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 67.93 (11) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 21 | |
MALE | 38 | |
Significant markers | N = 1 | |
Higher in MALE | 0 | |
Higher in FEMALE | 1 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
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KIF4B | -9.02 | 4.587e-11 | 7.96e-07 | 0.9662 |
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Expresson data file = BLCA.meth.for_correlation.filtered_data.txt
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Clinical data file = BLCA.clin.merged.picked.txt
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Number of patients = 59
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Number of genes = 17353
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Number of clinical features = 4
For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels
For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R
For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.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. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.