This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 19721 genes and 3 clinical features across 104 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.
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4 genes correlated to 'GENDER'.
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ALG11__2 , UTP14C , FAM35A , GLUD1
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No genes correlated to 'Time to Death', and 'AGE'.
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=4 | male | N=2 | female | N=2 |
Time to Death | Duration (Months) | 0.1-143.4 (median=18.1) |
censored | N = 73 | |
death | N = 31 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 62.32 (13) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 55 | |
MALE | 49 | |
Significant markers | N = 4 | |
Higher in MALE | 2 | |
Higher in FEMALE | 2 |
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Expresson data file = SARC-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = SARC-TP.merged_data.txt
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Number of patients = 104
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Number of genes = 19721
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Number of clinical features = 3
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.
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.