{"id":"https://openalex.org/W2922706703","doi":"https://doi.org/10.1093/bib/bbz028","title":"Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes","display_name":"Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes","publication_year":2019,"publication_date":"2019-02-22","ids":{"openalex":"https://openalex.org/W2922706703","doi":"https://doi.org/10.1093/bib/bbz028","mag":"2922706703","pmid":"https://pubmed.ncbi.nlm.nih.gov/30895300"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz028","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz028","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013525080","display_name":"F\u00e1bio Fabris","orcid":"https://orcid.org/0000-0001-7159-4668"},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Fabio Fabris","raw_affiliation_strings":["School of Computing, University of Kent, Kent, CT2 7NF, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of Kent, Kent, CT2 7NF, UK","institution_ids":["https://openalex.org/I20581793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025272654","display_name":"Daniel H. Palmer","orcid":"https://orcid.org/0000-0002-5766-9990"},"institutions":[{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]},{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel Palmer","raw_affiliation_strings":["Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK"],"affiliations":[{"raw_affiliation_string":"Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK","institution_ids":["https://openalex.org/I146655781","https://openalex.org/I4210151791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054858013","display_name":"Jo\u00e3o Pedro de Magalh\u00e3es","orcid":"https://orcid.org/0000-0002-6363-2465"},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]},{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o Pedro de Magalh\u00e3es","raw_affiliation_strings":["Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK"],"affiliations":[{"raw_affiliation_string":"Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK","institution_ids":["https://openalex.org/I146655781","https://openalex.org/I4210151791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087201377","display_name":"Alex A. Freitas","orcid":"https://orcid.org/0000-0001-9825-4700"},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alex A Freitas","raw_affiliation_strings":["School of Computing, University of Kent, Kent, CT2 7NF, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of Kent, Kent, CT2 7NF, UK","institution_ids":["https://openalex.org/I20581793"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5013525080"],"corresponding_institution_ids":["https://openalex.org/I20581793"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.942,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.74019417,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"21","issue":"3","first_page":"803","last_page":"814"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9979000091552734,"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":0.9947999715805054,"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/gene","display_name":"Gene","score":0.592265248298645},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5492420792579651},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5429695248603821},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4525515139102936},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3448311686515808},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32369863986968994}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.592265248298645},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5492420792579651},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5429695248603821},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4525515139102936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3448311686515808},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32369863986968994}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbz028","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz028","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30895300","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30895300","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:kar.kent.ac.uk:73238","is_oa":false,"landing_page_url":"https://kar.kent.ac.uk/73238/","pdf_url":null,"source":{"id":"https://openalex.org/S4377196264","display_name":"Kent Academic Repository (University of Kent)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20581793","host_organization_name":"University of Kent","host_organization_lineage":["https://openalex.org/I20581793"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7400000095367432}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":86,"referenced_works":["https://openalex.org/W605727707","https://openalex.org/W608314793","https://openalex.org/W1505191356","https://openalex.org/W1511986666","https://openalex.org/W1570448133","https://openalex.org/W1737699519","https://openalex.org/W1848567445","https://openalex.org/W1892189893","https://openalex.org/W1965302838","https://openalex.org/W1983463159","https://openalex.org/W1989277387","https://openalex.org/W1996202672","https://openalex.org/W2007587510","https://openalex.org/W2034613288","https://openalex.org/W2045949302","https://openalex.org/W2054673300","https://openalex.org/W2060987350","https://openalex.org/W2095720871","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2103632489","https://openalex.org/W2107356028","https://openalex.org/W2118659478","https://openalex.org/W2123336312","https://openalex.org/W2125121177","https://openalex.org/W2127072844","https://openalex.org/W2127875809","https://openalex.org/W2129559232","https://openalex.org/W2130410032","https://openalex.org/W2131856634","https://openalex.org/W2133465414","https://openalex.org/W2133990480","https://openalex.org/W2134736660","https://openalex.org/W2137937261","https://openalex.org/W2138075827","https://openalex.org/W2139843103","https://openalex.org/W2144600435","https://openalex.org/W2150766729","https://openalex.org/W2158217645","https://openalex.org/W2159482845","https://openalex.org/W2160356737","https://openalex.org/W2164005910","https://openalex.org/W2182361439","https://openalex.org/W2227395312","https://openalex.org/W2232370058","https://openalex.org/W2233603983","https://openalex.org/W2293040502","https://openalex.org/W2311607323","https://openalex.org/W2342127666","https://openalex.org/W2513896837","https://openalex.org/W2537623931","https://openalex.org/W2557283755","https://openalex.org/W2562319768","https://openalex.org/W2577490495","https://openalex.org/W2586852922","https://openalex.org/W2592659532","https://openalex.org/W2604504584","https://openalex.org/W2608595939","https://openalex.org/W2624280676","https://openalex.org/W2657631929","https://openalex.org/W2733047156","https://openalex.org/W2751302235","https://openalex.org/W2782511968","https://openalex.org/W2789939795","https://openalex.org/W2792808664","https://openalex.org/W2793643126","https://openalex.org/W2795073885","https://openalex.org/W2805310212","https://openalex.org/W2915536738","https://openalex.org/W2949093503","https://openalex.org/W2953367535","https://openalex.org/W2964257300","https://openalex.org/W3151854828","https://openalex.org/W4232478844","https://openalex.org/W4233698560","https://openalex.org/W4245055982","https://openalex.org/W4294216483","https://openalex.org/W6678058232","https://openalex.org/W6685961532","https://openalex.org/W6689011434","https://openalex.org/W6698064614","https://openalex.org/W6726515355","https://openalex.org/W6736610077","https://openalex.org/W6740358315","https://openalex.org/W6741091983","https://openalex.org/W6749036869"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"Biologists":[0],"very":[1],"often":[2],"use":[3,63,106],"enrichment":[4,36,71,108,142,184],"methods":[5,111,164,200],"based":[6,39],"on":[7,40],"statistical":[8,42],"hypothesis":[9],"tests":[10],"to":[11,51,77,138],"identify":[12,52],"gene":[13,90,167,172],"properties":[14,168],"that":[15,169,203],"are":[16,44,75,84],"significantly":[17],"over-represented":[18],"in":[19,54,208],"a":[20,30,97,118,177],"given":[21],"set":[22,32,178],"of":[23,25,33,80,86,89,93,104,120,127,130,134,160,163,179,196,199],"genes":[24],"interest,":[26],"by":[27,189],"comparison":[28],"with":[29],"'background'":[31],"genes.":[34],"These":[35],"methods,":[37,72,145],"although":[38],"rigorous":[41],"foundations,":[43],"not":[45],"always":[46],"the":[47,67,102,123,152,191,194],"best":[48],"single":[49],"option":[50],"patterns":[53],"biological":[55],"data.":[56],"In":[57,99],"many":[58],"cases,":[59],"one":[60,94],"can":[61],"also":[62],"classification":[64,73,110,144,186],"algorithms":[65,74],"from":[66],"machine-learning":[68],"field.":[69],"Unlike":[70],"designed":[76],"maximize":[78],"measures":[79],"predictive":[81],"performance":[82],"and":[83,115,125,140,143,158,185,193],"capable":[85],"analysing":[87],"combinations":[88],"properties,":[91],"instead":[92],"property":[95],"at":[96],"time.":[98],"practice,":[100],"however,":[101],"majority":[103],"studies":[105],"either":[107],"or":[109],"(rather":[112],"than":[113],"both),":[114],"there":[116],"is":[117,137],"lack":[119],"literature":[121],"discussing":[122],"pros":[124],"cons":[126],"both":[128,161,197,204],"types":[129,162,198],"method.":[131],"The":[132],"goal":[133],"this":[135],"paper":[136],"compare":[139],"contrast":[141],"offering":[146],"two":[147],"contributions.":[148],"First,":[149],"we":[150,175,201],"discuss":[151],"(to":[153],"some":[154],"extent":[155],"complementary)":[156],"advantages":[157],"disadvantages":[159],"for":[165,182],"identifying":[166],"discriminate":[170],"between":[171],"classes.":[173],"Second,":[174],"provide":[176],"high-level":[180],"recommendations":[181],"using":[183],"methods.":[187],"Overall,":[188],"highlighting":[190],"strengths":[192],"weaknesses":[195],"argue":[202],"should":[205],"be":[206],"used":[207],"bioinformatics":[209],"analyses.":[210]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
