{"id":"https://openalex.org/W4220684489","doi":"https://doi.org/10.1371/journal.pcbi.1009935","title":"Urgent need for consistent standards in functional enrichment analysis","display_name":"Urgent need for consistent standards in functional enrichment analysis","publication_year":2022,"publication_date":"2022-03-09","ids":{"openalex":"https://openalex.org/W4220684489","doi":"https://doi.org/10.1371/journal.pcbi.1009935","pmid":"https://pubmed.ncbi.nlm.nih.gov/35263338"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009935","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009935","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1009935","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044568728","display_name":"Kaumadi Wijesooriya","orcid":"https://orcid.org/0000-0002-1777-4964"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kaumadi Wijesooriya","raw_affiliation_strings":["Deakin University, School of Life and Environmental Sciences, Geelong, Australia"],"raw_orcid":"https://orcid.org/0000-0002-1777-4964","affiliations":[{"raw_affiliation_string":"Deakin University, School of Life and Environmental Sciences, Geelong, Australia","institution_ids":["https://openalex.org/I149704539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037626395","display_name":"Sameer A. Jadaan","orcid":"https://orcid.org/0000-0002-3047-8887"},"institutions":[{"id":"https://openalex.org/I4210115078","display_name":"Middle Technical University","ror":"https://ror.org/02fvkg758","country_code":"IQ","type":"education","lineage":["https://openalex.org/I4210115078"]}],"countries":["IQ"],"is_corresponding":false,"raw_author_name":"Sameer A. Jadaan","raw_affiliation_strings":["College of Health and Medical Technology, Middle Technical University, Baghdad, Iraq"],"raw_orcid":"https://orcid.org/0000-0002-3047-8887","affiliations":[{"raw_affiliation_string":"College of Health and Medical Technology, Middle Technical University, Baghdad, Iraq","institution_ids":["https://openalex.org/I4210115078"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034086666","display_name":"Kaushalya L. Perera","orcid":"https://orcid.org/0000-0002-1232-2627"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kaushalya L. Perera","raw_affiliation_strings":["Deakin University, School of Life and Environmental Sciences, Geelong, Australia"],"raw_orcid":"https://orcid.org/0000-0002-1232-2627","affiliations":[{"raw_affiliation_string":"Deakin University, School of Life and Environmental Sciences, Geelong, Australia","institution_ids":["https://openalex.org/I149704539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065485995","display_name":"Tanuveer Kaur","orcid":"https://orcid.org/0000-0003-3637-4007"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Tanuveer Kaur","raw_affiliation_strings":["Deakin University, School of Life and Environmental Sciences, Geelong, Australia"],"raw_orcid":"https://orcid.org/0000-0003-3637-4007","affiliations":[{"raw_affiliation_string":"Deakin University, School of Life and Environmental Sciences, Geelong, Australia","institution_ids":["https://openalex.org/I149704539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017271798","display_name":"Mark Ziemann","orcid":"https://orcid.org/0000-0002-7688-6974"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Mark Ziemann","raw_affiliation_strings":["Deakin University, School of Life and Environmental Sciences, Geelong, Australia"],"raw_orcid":"https://orcid.org/0000-0002-7688-6974","affiliations":[{"raw_affiliation_string":"Deakin University, School of Life and Environmental Sciences, Geelong, Australia","institution_ids":["https://openalex.org/I149704539"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5017271798"],"corresponding_institution_ids":["https://openalex.org/I149704539"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":11.3703,"has_fulltext":false,"cited_by_count":130,"citation_normalized_percentile":{"value":0.99220172,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"18","issue":"3","first_page":"e1009935","last_page":"e1009935"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.989300012588501,"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/popularity","display_name":"Popularity","score":0.5745474696159363},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5717124342918396},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5602669715881348},{"id":"https://openalex.org/keywords/bibliometrics","display_name":"Bibliometrics","score":0.5316489338874817},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.4764193296432495},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4561544954776764},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.454493910074234},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39531654119491577},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3727671802043915},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3675781786441803},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24993517994880676},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22951549291610718},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.18403416872024536},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16458925604820251}],"concepts":[{"id":"https://openalex.org/C2780586970","wikidata":"https://www.wikidata.org/wiki/Q1357284","display_name":"Popularity","level":2,"score":0.5745474696159363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5717124342918396},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5602669715881348},{"id":"https://openalex.org/C178315738","wikidata":"https://www.wikidata.org/wiki/Q603441","display_name":"Bibliometrics","level":2,"score":0.5316489338874817},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.4764193296432495},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4561544954776764},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.454493910074234},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39531654119491577},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3727671802043915},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3675781786441803},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24993517994880676},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22951549291610718},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.18403416872024536},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16458925604820251},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009935","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009935","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35263338","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35263338","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:dro.deakin.edu.au:DU:30165092","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401102","display_name":"Own your potential (DEAKIN)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149704539","host_organization_name":"Deakin University","host_organization_lineage":["https://openalex.org/I149704539"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8936487","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8936487","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:91a9e0feda9243f9a8f7426a09fd58f8","is_oa":true,"landing_page_url":"https://doaj.org/article/91a9e0feda9243f9a8f7426a09fd58f8","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 3, p e1009935 (2022)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/20611008","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Urgent_need_for_consistent_standards_in_functional_enrichment_analysis/20611008","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009935","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009935","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5600000023841858,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320971","display_name":"Monash University","ror":"https://ror.org/02bfwt286"},{"id":"https://openalex.org/F4320331131","display_name":"Australian Research Data Commons","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1535641839","https://openalex.org/W1544923801","https://openalex.org/W1989277387","https://openalex.org/W1993760308","https://openalex.org/W2008985174","https://openalex.org/W2027895157","https://openalex.org/W2035618305","https://openalex.org/W2045729458","https://openalex.org/W2077135570","https://openalex.org/W2078284062","https://openalex.org/W2100599058","https://openalex.org/W2103017472","https://openalex.org/W2107684775","https://openalex.org/W2117131533","https://openalex.org/W2127938920","https://openalex.org/W2128980492","https://openalex.org/W2130410032","https://openalex.org/W2134736660","https://openalex.org/W2155833028","https://openalex.org/W2159482845","https://openalex.org/W2179438025","https://openalex.org/W2214074259","https://openalex.org/W2283586982","https://openalex.org/W2294277978","https://openalex.org/W2342263667","https://openalex.org/W2345356016","https://openalex.org/W2546551333","https://openalex.org/W2752541434","https://openalex.org/W2795513215","https://openalex.org/W2931264270","https://openalex.org/W2957376989","https://openalex.org/W2962821542","https://openalex.org/W3016489853","https://openalex.org/W3037738062","https://openalex.org/W3039150496","https://openalex.org/W3043793521","https://openalex.org/W3125404605","https://openalex.org/W3136308181","https://openalex.org/W3153543576","https://openalex.org/W3159410008","https://openalex.org/W4231254854","https://openalex.org/W4237335579","https://openalex.org/W4294216483","https://openalex.org/W6813094581"],"related_works":["https://openalex.org/W2368605798","https://openalex.org/W2518037665","https://openalex.org/W2348524959","https://openalex.org/W2368049389","https://openalex.org/W2170801710","https://openalex.org/W2384861574","https://openalex.org/W2952704802","https://openalex.org/W4294565801","https://openalex.org/W2142306706","https://openalex.org/W2477036161"],"abstract_inverted_index":{"Gene":[0],"set":[1],"enrichment":[2,6,82,165,175,191],"tests":[3,92,116],"(a.k.a.":[4],"functional":[5,81,174],"analysis)":[7],"are":[8,22,27,38,147],"among":[9],"the":[10,32,43,63,69,107,128,132,185],"most":[11,172],"frequently":[12],"used":[13],"methods":[14,26,129],"in":[15,68,106,119,127],"computational":[16],"biology.":[17],"Despite":[18],"this":[19,105,141],"popularity,":[20],"there":[21],"concerns":[23],"that":[24,86,144],"these":[25,66,145],"being":[28],"applied":[29],"incorrectly":[30],"and":[31,56,134],"results":[33,168],"of":[34,45,51,58,65,75,88,121,140,164],"some":[35],"peer-reviewed":[36],"publications":[37],"unreliable.":[39],"These":[40],"problems":[41,146],"include":[42],"use":[44],"inappropriate":[46],"background":[47,98],"gene":[48,99,135],"lists,":[49],"lack":[50,57],"false":[52],"discovery":[53],"rate":[54],"correction":[55,113],"methodological":[59],"detail.":[60],"To":[61],"ascertain":[62],"frequency":[64],"issues":[67],"literature,":[70],"we":[71,161],"performed":[72],"a":[73],"screen":[74],"186":[76],"open-access":[77],"research":[78],"articles":[79],"describing":[80],"results.":[83],"We":[84],"find":[85],"95%":[87],"analyses":[89],"using":[90],"over-representation":[91],"did":[93,102],"not":[94,103,148],"implement":[95],"an":[96],"appropriate":[97],"list":[100],"or":[101,152,180],"describe":[104],"methods.":[108],"Failure":[109],"to":[110],"perform":[111],"p-value":[112],"for":[114,187,190],"multiple":[115],"was":[117],"identified":[118],"43%":[120],"analyses.":[122],"Many":[123],"studies":[124,176],"lacked":[125],"detail":[126],"section":[130],"about":[131],"tools":[133,166],"sets":[136],"used.":[137],"An":[138],"extension":[139],"survey":[142],"showed":[143],"associated":[149],"with":[150],"journal":[151],"article":[153],"level":[154],"bibliometrics.":[155],"Using":[156],"seven":[157],"independent":[158],"RNA-seq":[159],"datasets,":[160],"show":[162],"misuse":[163],"alters":[167],"substantially.":[169],"In":[170],"conclusion,":[171],"published":[173],"suffered":[177],"from":[178],"one":[179],"more":[181],"major":[182],"flaws,":[183],"highlighting":[184],"need":[186],"stronger":[188],"standards":[189],"analysis.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":36},{"year":2024,"cited_by_count":47},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":11}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
