{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T08:51:41Z","timestamp":1762678301172,"version":"build-2065373602"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T00:00:00Z","timestamp":1761523200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH-NCI","award":["R21TW012092"],"award-info":[{"award-number":["R21TW012092"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Pathway enrichment analysis is commonly used to interpret epigenomewide association studies, yet conventional methods often rely on arbitrary thresholds and simplified CpG\u2013gene mappings, making them sensitive to analytical choices and unable to fully leverage CpG\u2013gene 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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 The version of the code corresponding to this manuscript has been archived on Zenodo (https:\/\/doi.org\/10.5281\/zenodo.17209507).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf590","type":"journal-article","created":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T11:59:13Z","timestamp":1761393553000},"source":"Crossref","is-referenced-by-count":0,"title":["PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2006-7320","authenticated-orcid":false,"given":"Yinan","family":"Zheng","sequence":"first","affiliation":[{"name":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1641-2101","authenticated-orcid":false,"given":"Feng","family":"Gao","sequence":"additional","affiliation":[{"name":"Fielding School of Public Health, University of California , Los Angeles, Los Angeles, CA 90095,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lifang","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,10,27]]},"reference":[{"key":"2025110903495251200_btaf590-B1","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/s41598-021-04346-w","article-title":"The impact of methodology on the reproducibility and rigor of DNA methylation 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