{"id":"https://openalex.org/W4415615041","doi":"https://doi.org/10.1093/bioinformatics/btaf590","title":"PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework","display_name":"PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework","publication_year":2025,"publication_date":"2025-10-25","ids":{"openalex":"https://openalex.org/W4415615041","doi":"https://doi.org/10.1093/bioinformatics/btaf590","pmid":"https://pubmed.ncbi.nlm.nih.gov/41143682"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf590","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf590","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf590/64956803/btaf590.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf590/64956803/btaf590.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044839854","display_name":"Yinan Zheng","orcid":"https://orcid.org/0000-0002-2006-7320"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinan Zheng","raw_affiliation_strings":["Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,"],"raw_orcid":"https://orcid.org/0000-0002-2006-7320","affiliations":[{"raw_affiliation_string":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Feng Gao","orcid":"https://orcid.org/0000-0002-1641-2101"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Feng Gao","raw_affiliation_strings":["Fielding School of Public Health, University of California , Los Angeles, Los Angeles, CA 90095,"],"raw_orcid":"https://orcid.org/0000-0002-1641-2101","affiliations":[{"raw_affiliation_string":"Fielding School of Public Health, University of California , Los Angeles, Los Angeles, CA 90095,","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101012045","display_name":"Lifang Hou","orcid":null},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lifang Hou","raw_affiliation_strings":["Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , Chicago, IL 60611,","institution_ids":["https://openalex.org/I111979921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23017986,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.19859999418258667,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0786999985575676,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6937000155448914},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6836000084877014},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.589900016784668},{"id":"https://openalex.org/keywords/voting","display_name":"Voting","score":0.5688999891281128},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4814000129699707},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4722000062465668}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7501999735832214},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6937000155448914},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6836000084877014},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.589900016784668},{"id":"https://openalex.org/C520049643","wikidata":"https://www.wikidata.org/wiki/Q189760","display_name":"Voting","level":3,"score":0.5688999891281128},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4814000129699707},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4722000062465668},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46480000019073486},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.43950000405311584},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.40950000286102295},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.38530001044273376},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3700000047683716},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3127000033855438},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2768999934196472},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2702000141143799},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.26010000705718994}],"mesh":[{"descriptor_ui":"D000096264","descriptor_name":"Voting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000096264","descriptor_name":"Voting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000096264","descriptor_name":"Voting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf590","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf590","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf590/64956803/btaf590.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41143682","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41143682","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11405526","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12596613","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf590","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf590","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf590/64956803/btaf590.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415615041.pdf","grobid_xml":"https://content.openalex.org/works/W4415615041.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1979594866","https://openalex.org/W2152656267","https://openalex.org/W2172557341","https://openalex.org/W2333286569","https://openalex.org/W2907099021","https://openalex.org/W2910111050","https://openalex.org/W3126160703","https://openalex.org/W4205858977","https://openalex.org/W4282835344","https://openalex.org/W4385723965"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Pathway":[1],"enrichment":[2,61,97],"analysis":[3],"is":[4,103],"commonly":[5],"used":[6],"to":[7,27,32,50,80,122],"interpret":[8],"epigenomewide":[9],"association":[10],"studies,":[11],"yet":[12],"conventional":[13],"methods":[14],"often":[15],"rely":[16],"on":[17,88,106,128],"arbitrary":[18,89],"thresholds":[19],"and":[20,30,76,91,94,113],"simplified":[21],"CpG-gene":[22,35],"mappings,":[23,53],"making":[24],"them":[25],"sensitive":[26],"analytical":[28],"choices":[29],"unable":[31],"fully":[33],"leverage":[34],"relationships":[36],"Recent":[37],"advances":[38],"in":[39,58],"expression":[40],"quantitative":[41],"trait":[42],"methylation":[43,60],"(eQTM)":[44],"studies":[45],"offer":[46],"a":[47,72],"rich":[48],"resource":[49],"refine":[51],"these":[52],"but":[54],"are":[55],"rarely":[56],"utilized":[57],"DNA":[59],"pipelines.":[62],"RESULTS:":[63],"We":[64],"developed":[65],"PathwayVote,":[66],"an":[67],"R":[68],"package":[69],"that":[70],"implements":[71],"voting-based":[73],"consensus":[74],"approach":[75],"leverages":[77],"eQTM":[78],"data":[79],"identify":[81],"robustly":[82],"enriched":[83],"pathways.":[84],"PathwayVote":[85,102],"reduces":[86],"dependence":[87],"cutoffs":[90],"improves":[92],"sensitivity":[93],"reproducibility":[95],"of":[96,118],"results.":[98],"AVAILABILITY":[99],"AND":[100],"IMPLEMENTATION:":[101],"freely":[104],"available":[105],"GitHub":[107],"(https://github.com/YinanZheng/PathwayVote)":[108],"under":[109],"the":[110,119],"GPL-3":[111],"license":[112],"CRAN:":[114],"https://CRAN.R-project.org/package=PathwayVote.":[115],"The":[116],"version":[117],"code":[120],"corresponding":[121],"this":[123],"manuscript":[124],"has":[125],"been":[126],"archived":[127],"Zenodo":[129],"(https://doi.org/10.5281/zenodo.17209507).":[130]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-28T00:00:00"}
