{"id":"https://openalex.org/W4224078189","doi":"https://doi.org/10.1109/tcbb.2022.3167245","title":"exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data","display_name":"exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data","publication_year":2022,"publication_date":"2022-04-13","ids":{"openalex":"https://openalex.org/W4224078189","doi":"https://doi.org/10.1109/tcbb.2022.3167245","pmid":"https://pubmed.ncbi.nlm.nih.gov/35417352"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3167245","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3167245","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Leandro Di Persia","orcid":null},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Leandro Di Persia","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tiago Lopez","orcid":null},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Tiago Lopez","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Agustin Arce","orcid":"https://orcid.org/0000-0003-3619-3898"},"institutions":[{"id":"https://openalex.org/I4210149924","display_name":"Instituto de Agrobiotecnolog\u00eda del Litoral","ror":"https://ror.org/057915t59","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I3121987637","https://openalex.org/I4210087694","https://openalex.org/I4210123736","https://openalex.org/I4210149924","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Agustin Arce","raw_affiliation_strings":["Instituto de Agrobiotecnologia del Litoral, IAL, UNL-CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina"],"raw_orcid":"https://orcid.org/0000-0003-3619-3898","affiliations":[{"raw_affiliation_string":"Instituto de Agrobiotecnologia del Litoral, IAL, UNL-CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina","institution_ids":["https://openalex.org/I4210149924"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Diego H. Milone","orcid":"https://orcid.org/0000-0003-2182-4351"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Diego H. Milone","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina"],"raw_orcid":"https://orcid.org/0000-0003-2182-4351","affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"last","author":{"id":null,"display_name":"Georgina Stegmayer","orcid":"https://orcid.org/0000-0003-4459-4560"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Georgina Stegmayer","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina"],"raw_orcid":"https://orcid.org/0000-0003-4459-4560","affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina","institution_ids":["https://openalex.org/I151201029"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3921,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.5324395,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"2","first_page":"999","last_page":"1008"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9404000043869019,"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":0.9404000043869019,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.04089999943971634,"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":0.0035000001080334187,"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/inference","display_name":"Inference","score":0.6238999962806702},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6069999933242798},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5428000092506409},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5364999771118164},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5349000096321106},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.508899986743927},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4124999940395355},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.3853999972343445},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.38530001044273376}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7332000136375427},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6238999962806702},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6069999933242798},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5666000247001648},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5428000092506409},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5364999771118164},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5349000096321106},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.508899986743927},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4124999940395355},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.3853999972343445},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.38530001044273376},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.3846000134944916},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.36980000138282776},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36719998717308044},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.36399999260902405},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36230000853538513},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3549000024795532},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.3425999879837036},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.3212999999523163},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.31869998574256897},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.31209999322891235},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.30570000410079956},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.289000004529953},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.28529998660087585},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.2838999927043915},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.28139999508857727},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.2590000033378601},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.2583000063896179}],"mesh":[{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3167245","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3167245","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35417352","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35417352","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1217372451","display_name":null,"funder_award_id":"CAI+D 2020 115","funder_id":"https://openalex.org/F4320323408","funder_display_name":"Universidad Nacional del Litoral"},{"id":"https://openalex.org/G3034095715","display_name":null,"funder_award_id":"AC-00010-18","funder_id":"https://openalex.org/F4320329199","funder_display_name":"Agencia Santafesina de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n"},{"id":"https://openalex.org/G3489732522","display_name":null,"funder_award_id":"PICT 2018-3384","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G8732257632","display_name":null,"funder_award_id":"117/14","funder_id":"https://openalex.org/F4320329199","funder_display_name":"Agencia Santafesina de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320323408","display_name":"Universidad Nacional del Litoral","ror":"https://ror.org/00pt8r998"},{"id":"https://openalex.org/F4320329199","display_name":"Agencia Santafesina de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n","ror":null},{"id":"https://openalex.org/F4320334832","display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","ror":"https://ror.org/03stxzb56"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W183401690","https://openalex.org/W1504886279","https://openalex.org/W1565746575","https://openalex.org/W1597559145","https://openalex.org/W1659833910","https://openalex.org/W1895597370","https://openalex.org/W1902027874","https://openalex.org/W1995242543","https://openalex.org/W2021105899","https://openalex.org/W2036450478","https://openalex.org/W2043545458","https://openalex.org/W2045156863","https://openalex.org/W2055043387","https://openalex.org/W2082607144","https://openalex.org/W2084168100","https://openalex.org/W2107665951","https://openalex.org/W2108919995","https://openalex.org/W2117486996","https://openalex.org/W2138842411","https://openalex.org/W2150926065","https://openalex.org/W2151723682","https://openalex.org/W2152828463","https://openalex.org/W2155440340","https://openalex.org/W2166664936","https://openalex.org/W2169896388","https://openalex.org/W2323179903","https://openalex.org/W2404400936","https://openalex.org/W2775315818","https://openalex.org/W2887057068","https://openalex.org/W2989608901","https://openalex.org/W4236358448","https://openalex.org/W7010034787"],"related_works":[],"abstract_inverted_index":{"The":[0,89,141],"computational":[1,54],"methods":[2,96],"for":[3,53,76],"the":[4,30,38,64,81,103,110,121],"prediction":[5,111],"of":[6,21,34,66,83,112,134,143],"gene":[7,17,68],"function":[8],"annotations":[9,36,61,78,114],"aim":[10],"to":[11,117],"automatically":[12],"find":[13],"associations":[14],"between":[15],"a":[16,19,51,73,126],"and":[18,37,46,62,137,149],"set":[20],"Gene":[22],"Ontology":[23],"(GO)":[24],"terms":[25],"describing":[26],"its":[27],"functions.":[28,69,140],"Since":[29],"hand-made":[31],"curation":[32],"process":[33],"novel":[35,74,90],"corresponding":[39],"wet":[40],"experiments":[41],"validations":[42],"are":[43],"very":[44],"time-consuming":[45],"costly":[47],"procedures,":[48],"there":[49],"is":[50,151],"need":[52],"tools":[55],"that":[56],"can":[57],"reliably":[58],"predict":[59],"likely":[60],"boost":[63],"discovery":[65],"new":[67],"This":[70],"work":[71],"proposes":[72],"method":[75,91],"predicting":[77,135],"based":[79],"on":[80,97],"inference":[82],"GO":[84,113],"similarities":[85],"from":[86],"expression":[87],"similarities.":[88],"was":[92,123,132],"benchmarked":[93],"against":[94],"other":[95],"several":[98],"public":[99],"biological":[100,139],"datasets,":[101],"obtaining":[102],"best":[104],"comparative":[105],"results.":[106],"exp2GO":[107],"effectively":[108],"improved":[109],"in":[115],"comparison":[116],"state-of-the-art":[118],"methods.":[119],"Furthermore,":[120],"proposal":[122],"validated":[124],"with":[125],"full":[127,147],"genome":[128],"case":[129],"where":[130],"it":[131],"capable":[133],"relevant":[136],"accurate":[138],"repository":[142],"this":[144],"project":[145],"withh":[146],"data":[148],"code":[150],"available":[152],"at":[153],"https://github.com/sinc-lab/exp2GO.":[154]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2022-04-19T00:00:00"}
