DMRforPairs

DMRforPairs identifies differentially methylated regions between unique sample pairs to enable regional comparison of DNA methylation profiles from Illumina Infinium HumanMethylation450 BeadChip data.

Key Features:

• Pairwise sample comparison: Performs direct comparison of regional methylation between two unique samples without requiring sample groups.
• Probe-dense region identification: Detects genomic regions with sufficient probe density based on probe proximity on the Illumina HumanMethylation450 array.
• Region-level differential methylation evaluation: Compares methylation values across identified regions rather than individual CpG loci to define DMRs between samples.
• Functional probe annotation: Optionally annotates probes within regions to functional classes for contextual interpretation.
• Visualization of DMRs: Produces outputs representing identified differentially methylated regions for interpretation relative to sample phenotype or origin.

Scientific Applications:

• Individual-pair epigenetic comparison: Enables methylation comparisons for rare diseases, unique patient-derived cell lines, or single-case studies where large cohorts are unavailable.
• Developmental and phenotypic studies: Supports analysis of epigenetic differences across specific developmental stages or phenotypic contrasts at the sample-pair level.
• Cell line benchmarking: Has been applied to public data from four human cell lines (two lymphoblastoid lines and two cancer lines, A431 and MCF7) and identified increasing numbers of DMRs as biological similarity between samples decreased.

Methodology:

Identifies probe-dense genomic regions from Illumina Infinium HumanMethylation450 BeadChip probe positions, optionally annotates probes to functional classes, and evaluates differential methylation by comparing methylation values across those regions between individual samples.