This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17336 genes and 7 clinical features across 85 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.
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5 genes correlated to 'GENDER'.
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KIF4B , METAP2 , B3GNT1 , UTP14C , KRT79
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No genes correlated to 'Time to Death', 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', 'NUMBERPACKYEARSSMOKED', 'STOPPEDSMOKINGYEAR', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
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=5 | male | N=2 | female | N=3 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
STOPPEDSMOKINGYEAR | Spearman correlation test | N=0 | ||||
TOBACCOSMOKINGHISTORYINDICATOR | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0.4-118.9 (median=7.2) |
censored | N = 57 | |
death | N = 23 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 66.67 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 26 | |
MALE | 59 | |
Significant markers | N = 5 | |
Higher in MALE | 2 | |
Higher in FEMALE | 3 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
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KIF4B | -10.25 | 1.729e-13 | 3e-09 | 0.9622 |
METAP2 | -6.07 | 5.253e-08 | 0.000911 | 0.8497 |
B3GNT1 | 6.02 | 1.171e-07 | 0.00203 | 0.854 |
UTP14C | 6.94 | 2.628e-07 | 0.00456 | 0.9289 |
KRT79 | -5.09 | 2.864e-06 | 0.0496 | 0.7862 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 78 (18) |
Significant markers | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 35.59 (23) |
Significant markers | N = 0 |
STOPPEDSMOKINGYEAR | Mean (SD) | 1991.39 (18) |
Significant markers | N = 0 |
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Expresson data file = BLCA-TP.meth.for_correlation.filtered_data.txt
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Clinical data file = BLCA-TP.clin.merged.picked.txt
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Number of patients = 85
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Number of genes = 17336
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Number of clinical features = 7
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.