coMET

coMET visualizes epigenome-wide association scan (EWAS) results, co-methylation patterns, and genomic annotations to aid interpretation of DNA methylation variation underlying complex traits.

Key Features:

• Regional Plot Generation: Generates detailed regional plots that display EWAS results for specified genomic regions and supports microarray and sequencing DNA methylation data including Illumina Infinium 450k, whole‑genome bisulfite sequencing (WGBS), and MeDIP‑seq.
• DNA Co-methylation Patterns: Estimates and visualizes pairwise correlations between CpG sites to reveal co-methylation patterns.
• Integration with Genomic Annotations: Overlays ENCODE-based annotations, gene tracks, reference CpG sites, and user-defined features onto plots.
• Versatility Across Data Types: Applies to diverse epigenetic and functional genomic datasets across multiple species.

Scientific Applications:

• EWAS interpretation: Facilitates interpretation of EWAS signals by combining regional association plots with co-methylation structure and annotation context.
• Functional annotation contextualization: Enables integration of ENCODE annotations and gene tracks to contextualize methylation–trait associations.
• Cross-species epigenomic analysis: Supports analysis of DNA methylation and other genomic datasets from non-human species.

Methodology:

Generates regional EWAS association plots, computes and visualizes CpG co‑methylation correlations, and overlays ENCODE annotations, gene tracks, reference CpG sites, and user‑defined features.