DMRfinder

DMRfinder identifies differentially methylated regions (DMRs) from bisulfite sequencing (MethylC-seq) data to quantify and compare DNA methylation across biological conditions.

Key Features:

• Efficient Post-Alignment Processing: Integrates post-alignment steps including extraction of methylation counts and preparation for statistical analysis.
• Modified Single-Linkage Clustering: Groups methylation sites into genomic regions using a modified single-linkage clustering approach.
• Statistical Analysis Framework: Applies beta-binomial hierarchical modeling and Wald tests to compare methylation levels and identify significant DMRs.
• Novel Methylation Site Analysis: Supports analysis of novel methylation sites detected in sequencing data.
• Methylation Linkage Examination: Examines methylation linkage to assess spatial organization of methylation patterns.
• Simultaneous Multi-Sample Group Analysis: Performs statistical comparisons across multiple sample groups concurrently.

Scientific Applications:

• Epigenetic research: Enables detection of DNA methylation dynamics in epigenetic studies.
• Gene regulation studies: Facilitates investigation of methylation-associated regulation of gene expression.
• Cancer biology: Supports identification of DMRs implicated in cancer epigenetics.
• Developmental biology: Used to analyze methylation changes across developmental stages.
• Disease association studies: Compares methylation between disease and control conditions to identify disease-associated epigenetic changes.

Methodology:

After alignment of bisulfite-treated (MethylC-seq) reads to a reference genome, DMRfinder extracts methylation counts, clusters sites with a modified single-linkage approach, and applies beta-binomial hierarchical modeling with Wald tests to identify significant DMRs.