BioMethyl: an R package for biological interpretation of DNA methylation data

Bioinformatics
Yue WangChao Cheng

Abstract

The accumulation of publicly available DNA methylation datasets has resulted in the need for tools to interpret the specific cellular phenotypes in bulk tissue data. Current approaches use either single differentially methylated CpG sites or differentially methylated regions that map to genes. However, these approaches may introduce biases in downstream analyses of biological interpretation, because of the variability in gene length. There is a lack of approaches to interpret DNA methylation effectively. Therefore, we have developed computational models to provide biological interpretation of relevant gene sets using DNA methylation data in the context of The Cancer Genome Atlas. We illustrate that Biological interpretation of DNA Methylation (BioMethyl) utilizes the complete DNA methylation data for a given cancer type to reflect corresponding gene expression profiles and performs pathway enrichment analyses, providing unique biological insight. Using breast cancer as an example, BioMethyl shows high consistency in the identification of enriched biological pathways from DNA methylation data compared to the results calculated from RNA sequencing data. We find that 12 out of 14 pathways identified by BioMethyl are shared with th...Continue Reading

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Datasets Mentioned

BETA
GSE42861
GSE15573

Methods Mentioned

BETA
RNA-seq

Software Mentioned

ENmix
Gene Set Enrichment Analysis ( GSEA )
GSEA
R package
BioMethyl package
BioMethyl R
Annotation
- Modules
R
BioMethyl

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