EpiMethEx

EpiMethEx performs integrated analysis of DNA methylation and gene expression as an R package to identify methylation hotspots and relate promoter hypomethylation and intragenic hypermethylation to gene regulation.

Key Features:

• Cyclic Correlation Analyses: Employs cyclic correlation analyses to explore relationships between methylation data and gene expression levels.
• Gene Stratification: Stratifies samples by gene expression levels to identify differentially expressed genes and associated methylation changes.
• Probeset Grouping by Genomic Position: Groups methylation probesets according to their relative positions within gene sequences to detect wide genomic methylation events related to genetic modulation.
• Identification of Methylation Hotspots: Identifies methylation hotspots associated with gene dysregulation that may serve as biomarkers or therapeutic targets.

Scientific Applications:

• Global methylation-expression association: Confirms negative associations between promoter hypomethylation and gene overexpression across multiple genes.
• Intragenic methylation analysis: Detects instances where intragenic hypermethylation is associated with sustained gene overexpression.
• Epigenetics and oncology research: Supports analyses relevant to epigenetics, oncology, and personalized medicine.

Methodology:

Samples are segmented/stratified by expression levels to identify differentially expressed genes; cyclic correlation analyses are applied to relate methylation and expression; methylation probesets modulated among gene-stratified samples are detected and grouped by genomic position to uncover significant methylation events.