Work

PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework

Year: 2025

Type: article

Abstract: MOTIVATION: Pathway enrichment analysis is commonly used to interpret epigenomewide association studies, yet conventional methods often rely on arbitrary thresholds and simplified CpG-gene mappings, making them sensitive to analytical choices and unable to fully leverage CpG-gene relationships Recent advances in expression quantitative trait methylation (eQTM) studies offer a rich resource to refine these mappings, but are rarely utilized in DNA methylation enrichment pipelines. RESULTS: We developed PathwayVote, an R package that implements a voting-based consensus approach and leverages eQTM data to identify robustly enriched pathways. PathwayVote reduces dependence on arbitrary cutoffs and improves sensitivity and reproducibility of enrichment results. AVAILABILITY AND IMPLEMENTATION: PathwayVote is freely available on GitHub (https://github.com/YinanZheng/PathwayVote) under the GPL-3 license and CRAN: https://CRAN.R-project.org/package=PathwayVote. The version of the code corresponding to this manuscript has been archived on Zenodo (https://doi.org/10.5281/zenodo.17209507).

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btaf590

Authors: Yinan Zheng, Feng Gao, Lifang Hou

Institutions: Northwestern University, University of California, Los Angeles

Language: English

Topic: Bioinformatics and Genomic Networks

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,989

Funders: National Institutes of Health, National Cancer Institute