{"id":"https://openalex.org/W4290973443","doi":"https://doi.org/10.1371/journal.pcbi.1010348","title":"Nine quick tips for pathway enrichment analysis","display_name":"Nine quick tips for pathway enrichment analysis","publication_year":2022,"publication_date":"2022-08-11","ids":{"openalex":"https://openalex.org/W4290973443","doi":"https://doi.org/10.1371/journal.pcbi.1010348","pmid":"https://pubmed.ncbi.nlm.nih.gov/35951505"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010348","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010348","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010348&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010348&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011556172","display_name":"Davide Chicco","orcid":"https://orcid.org/0000-0001-9655-7142"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Davide Chicco","raw_affiliation_strings":["Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078020905","display_name":"Giuseppe Agapito","orcid":"https://orcid.org/0000-0003-2868-7732"},"institutions":[{"id":"https://openalex.org/I36443711","display_name":"Magna Graecia University","ror":"https://ror.org/0530bdk91","country_code":"IT","type":"education","lineage":["https://openalex.org/I36443711"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giuseppe Agapito","raw_affiliation_strings":["Dipartimento di Giurisprudenza Economia e Sociologia, Universit\u00e0 Magna Graecia di Catanzaro, Catanzaro, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Giurisprudenza Economia e Sociologia, Universit\u00e0 Magna Graecia di Catanzaro, Catanzaro, Italy","institution_ids":["https://openalex.org/I36443711"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011556172"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.7288,"has_fulltext":true,"cited_by_count":74,"citation_normalized_percentile":{"value":0.97359389,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"18","issue":"8","first_page":"e1010348","last_page":"e1010348"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9951000213623047,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9750000238418579,"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/relevance","display_name":"Relevance (law)","score":0.6591830253601074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6221132278442383},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5083178877830505},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4988243579864502},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47040945291519165},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34680891036987305},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2952069044113159},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07646751403808594}],"concepts":[{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.6591830253601074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6221132278442383},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5083178877830505},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4988243579864502},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47040945291519165},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34680891036987305},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2952069044113159},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07646751403808594},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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":"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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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.1010348","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010348","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010348&type=printable","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:35951505","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35951505","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:RePEc:plo:pcbi00:1010348","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010348","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:boa.unimib.it:10281/430239","is_oa":true,"landing_page_url":"https://hdl.handle.net/10281/430239","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:e092150d53fa4680b06519f5ab703bd3","is_oa":true,"landing_page_url":"https://doaj.org/article/e092150d53fa4680b06519f5ab703bd3","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 8, p e1010348 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9371296","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9371296","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010348","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010348","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010348&type=printable","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4290973443.pdf","grobid_xml":"https://content.openalex.org/works/W4290973443.grobid-xml"},"referenced_works_count":115,"referenced_works":["https://openalex.org/W122167022","https://openalex.org/W1768179097","https://openalex.org/W1969353942","https://openalex.org/W1969709265","https://openalex.org/W1979594866","https://openalex.org/W1985213868","https://openalex.org/W1986849266","https://openalex.org/W1997921822","https://openalex.org/W2005918637","https://openalex.org/W2028133290","https://openalex.org/W2028689806","https://openalex.org/W2032350460","https://openalex.org/W2034543587","https://openalex.org/W2036318837","https://openalex.org/W2043029113","https://openalex.org/W2050200982","https://openalex.org/W2061912939","https://openalex.org/W2070050178","https://openalex.org/W2079031049","https://openalex.org/W2086744970","https://openalex.org/W2095900642","https://openalex.org/W2096173332","https://openalex.org/W2097948046","https://openalex.org/W2100980426","https://openalex.org/W2101536220","https://openalex.org/W2105924489","https://openalex.org/W2108096229","https://openalex.org/W2110687686","https://openalex.org/W2113624587","https://openalex.org/W2116443392","https://openalex.org/W2123106337","https://openalex.org/W2124649441","https://openalex.org/W2124954099","https://openalex.org/W2125011914","https://openalex.org/W2130410032","https://openalex.org/W2134582937","https://openalex.org/W2135805255","https://openalex.org/W2140503409","https://openalex.org/W2144981148","https://openalex.org/W2146276081","https://openalex.org/W2146980885","https://openalex.org/W2147714160","https://openalex.org/W2155833028","https://openalex.org/W2161336914","https://openalex.org/W2164298117","https://openalex.org/W2166373524","https://openalex.org/W2223119478","https://openalex.org/W2242206668","https://openalex.org/W2290195878","https://openalex.org/W2315135172","https://openalex.org/W2345356016","https://openalex.org/W2430130403","https://openalex.org/W2461732257","https://openalex.org/W2474747771","https://openalex.org/W2517051411","https://openalex.org/W2551432253","https://openalex.org/W2558585189","https://openalex.org/W2591941343","https://openalex.org/W2736848882","https://openalex.org/W2749320391","https://openalex.org/W2767914218","https://openalex.org/W2771169143","https://openalex.org/W2795490756","https://openalex.org/W2796231776","https://openalex.org/W2802802541","https://openalex.org/W2807134042","https://openalex.org/W2809000676","https://openalex.org/W2899942534","https://openalex.org/W2900569176","https://openalex.org/W2908895378","https://openalex.org/W2910111050","https://openalex.org/W2911094364","https://openalex.org/W2912936113","https://openalex.org/W2918086501","https://openalex.org/W2920342605","https://openalex.org/W2950595506","https://openalex.org/W2962821542","https://openalex.org/W2968022676","https://openalex.org/W2975578922","https://openalex.org/W2975738904","https://openalex.org/W2977489313","https://openalex.org/W2979345840","https://openalex.org/W2979832776","https://openalex.org/W2981347193","https://openalex.org/W2983485493","https://openalex.org/W2984996233","https://openalex.org/W2998008364","https://openalex.org/W3004505497","https://openalex.org/W3004695644","https://openalex.org/W3020992812","https://openalex.org/W3026082741","https://openalex.org/W3039150496","https://openalex.org/W3042896257","https://openalex.org/W3047745118","https://openalex.org/W3076622137","https://openalex.org/W3106377951","https://openalex.org/W3137181410","https://openalex.org/W3145969289","https://openalex.org/W3165739193","https://openalex.org/W3170940710","https://openalex.org/W3186118520","https://openalex.org/W3196948502","https://openalex.org/W3202413159","https://openalex.org/W3214475573","https://openalex.org/W3217314753","https://openalex.org/W4211039611","https://openalex.org/W4220684489","https://openalex.org/W4220895458","https://openalex.org/W4226298065","https://openalex.org/W4242856680","https://openalex.org/W6717823748","https://openalex.org/W6750147248","https://openalex.org/W6751069187","https://openalex.org/W6763355676","https://openalex.org/W6769546971"],"related_works":["https://openalex.org/W1585007175","https://openalex.org/W2382521049","https://openalex.org/W2144385241","https://openalex.org/W4300101996","https://openalex.org/W2165950148","https://openalex.org/W4253593777","https://openalex.org/W2951497643","https://openalex.org/W2085384747","https://openalex.org/W2088166309","https://openalex.org/W1891216533"],"abstract_inverted_index":{"Pathway":[0],"enrichment":[1,209],"analysis":[2],"(PEA)":[3],"is":[4,43],"a":[5,17,132,150,175,215],"computational":[6,72,115],"biology":[7],"method":[8],"that":[9,13,103,154],"identifies":[10],"biological":[11],"functions":[12,31],"are":[14,52,178],"overrepresented":[15],"in":[16,149],"group":[18],"of":[19,37,66,71,180,218],"genes":[20,38],"more":[21],"than":[22],"would":[23],"be":[24,157],"expected":[25],"by":[26,32,161],"chance":[27],"and":[28,48,81,113,129,141,159,165,187,211],"ranks":[29],"these":[30,94],"relevance.":[33],"The":[34],"relative":[35],"abundance":[36],"pertinent":[39],"to":[40,79,82,92,100,125,130,171,182,195,214],"specific":[41],"pathways":[42,51],"measured":[44],"through":[45],"statistical":[46],"methods,":[47],"associated":[49],"functional":[50],"retrieved":[53],"from":[54],"online":[55],"bioinformatics":[56,85],"databases.":[57],"In":[58],"the":[59,64,67],"last":[60],"decade,":[61],"along":[62],"with":[63],"spread":[65],"internet,":[68],"higher":[69],"availability":[70],"resources":[73],"made":[74],"PEA":[75,198],"software":[76],"tools":[77],"easy":[78],"access":[80],"use":[83,93],"for":[84,111],"practitioners":[86],"worldwide.":[87],"Although":[88],"it":[89,96],"became":[90,98],"easier":[91,99],"tools,":[95],"also":[97],"make":[101],"mistakes":[102,128],"could":[104],"generate":[105,184],"inflated":[106],"or":[107],"misleading":[108],"results,":[109,186],"especially":[110],"beginners":[112],"inexperienced":[114],"biologists.":[116],"With":[117],"this":[118],"article,":[119],"we":[120],"propose":[121],"nine":[122,147,201],"quick":[123],"tips":[124,168,202],"avoid":[126],"common":[127],"out":[131],"complete,":[133],"sound,":[134],"thorough":[135],"PEA,":[136,176],"which":[137],"can":[138,156,203],"produce":[139],"relevant":[140],"robust":[142],"results.":[143,199],"We":[144],"describe":[145],"our":[146],"guidelines":[148,190],"simple":[151],"way,":[152],"so":[153],"they":[155],"understood":[158],"used":[160],"anyone,":[162],"including":[163],"students":[164],"beginners.":[166],"Some":[167],"explain":[169],"what":[170],"do":[172],"before":[173],"starting":[174],"others":[177],"suggestions":[179],"how":[181],"correctly":[183],"meaningful":[185],"some":[188,192],"final":[189],"indicate":[191],"useful":[193],"steps":[194],"properly":[196],"interpret":[197],"Our":[200],"help":[204],"users":[205],"perform":[206],"better":[207,216],"pathway":[208],"analyses":[210],"eventually":[212],"contribute":[213],"understanding":[217],"current":[219],"biology.":[220]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":30},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":4}],"updated_date":"2026-04-12T07:58:50.170612","created_date":"2025-10-10T00:00:00"}
