GeneDMRs

GeneDMRs computes gene-based differentially methylated regions from NGS-based methylome data to quantify methylation across genes, gene bodies, promoters, exons, introns, CpG islands and their overlapping regions and to assess methylation effects on gene transcription.

Key Features:

• Comprehensive Methylation Analysis: Calculates methylation rates across genes, promoters, exons, introns, CpG islands, CpG island shores, and their overlapping regions.
• Differential Methylation Detection: Identifies differentially methylated regions and differentially methylated genes (DMG) based on genes, gene bodies, CpG islands, and their interactions.
• NGS Integration: Operates on NGS-based methylome data to support high-throughput methylation analyses.
• RRBS Case Study: Has been applied to reduced representation bisulfite sequencing (RRBS) data, including the public mouse dataset GSE62392, to reveal biologically significant methylation patterns.

Scientific Applications:

• Epigenetic Research: Investigate how differential methylation across genes and regulatory elements affects gene regulation.
• Disease Studies: Explore methylation changes associated with diseases to identify potential biomarkers or therapeutic targets.
• Developmental Biology: Study methylation dynamics during development and their impact on gene expression.

Methodology:

Calculates methylation rates for specified genomic regions and identifies differentially methylated regions based on genes (DMG), gene bodies, CpG islands, and their interactions.