FuncEpiMod

FuncEpiMod integrates Illumina Infinium HumanMethylation450 DNA methylation data with gene expression datasets to identify epigenetically regulated gene modules and molecular pathways.

Key Features:

• Integrative Analysis: Integrates Illumina Infinium HumanMethylation450 DNA methylation data with gene expression profiles for joint analysis.
• Identification of Gene Modules: Identifies modules of genes showing coordinated differential methylation and differential expression within the human interactome.
• Validation on Simulated and Real Data: Has been validated using both simulated datasets and real-world data to assess performance.
• Discovery of Novel Epigenetic Hotspots: Detects novel epigenetic hotspots and implicates regulators of tumor suppressor pathways, as demonstrated in endometrial cancer studies.
• Application in Cellular Differentiation Studies: Applied to identify gene expression markers and DNA methylation–influenced gene modules in endothelial cell subtypes.

Scientific Applications:

• Cancer Epigenetics: Identification of epigenetically deregulated genes, hotspots, and pathways in cancer, including endometrial cancer.
• Cellular Differentiation: Analysis of DNA methylation–driven gene modules and markers relevant to cellular differentiation such as endothelial cell subtype specification.
• Pathway and Driver Gene Discovery: Systems-level identification of key genes and signaling pathways potentially driven by epigenetic mechanisms.

Methodology:

Implements a functional supervised algorithm that analyzes Illumina Infinium HumanMethylation450 DNA methylation and gene expression data (matched or unmatched) within the context of the human interactome/protein-protein interactions to detect coordinated differential methylation and differential expression and derive functional gene modules.