PathwayVote

PathwayVote implements a voting-based consensus approach for robust pathway enrichment analysis of DNA methylation data, leveraging expression quantitative trait methylation (eQTM) data to refine CpG-gene mappings and reduce dependence on arbitrary thresholds.

Key Features:

• Voting-based consensus framework: Integrates multiple analytical perspectives to identify consistently enriched pathways and improve reproducibility of enrichment results.
• eQTM data integration: Leverages expression quantitative trait methylation data to refine CpG-gene regulatory mappings beyond simplified approaches.
• Probe bias correction: Addresses probe bias inherent in DNA methylation data to improve sensitivity of pathway detection.
• Reduced threshold dependence: Minimizes reliance on arbitrary cutoffs that conventional methods require for CpG selection and mapping.

Scientific Applications:

• Epigenome-wide association study interpretation: Enables robust pathway enrichment analysis of DNA methylation data from EWAS to identify biologically meaningful pathways.
• CpG-gene relationship analysis: Utilizes refined regulatory relationships between CpG sites and genes through eQTM-based mapping for improved biological inference.

Methodology:

PathwayVote implements a voting-based consensus approach that integrates CpG-gene regulatory information from eQTM studies to address probe bias and identify robustly enriched pathways.