This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 19848 genes and 3 clinical features across 61 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 1 clinical feature related to at least one genes.
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3 genes correlated to 'GENDER'.
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DKFZP434L187 , CHTF8 , HAS3
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No genes correlated to 'AGE', and 'RACE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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AGE | Spearman correlation test | N=0 | ||||
GENDER | Wilcoxon test | N=3 | male | N=3 | female | N=0 |
RACE | Kruskal-Wallis test | N=0 |
AGE | Mean (SD) | 49.31 (14) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 40 | |
MALE | 21 | |
Significant markers | N = 3 | |
Higher in MALE | 3 | |
Higher in FEMALE | 0 |
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Expresson data file = PCPG-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = PCPG-TP.merged_data.txt
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Number of patients = 61
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Number of genes = 19848
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Number of clinical features = 3
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 multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' 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.