{"id":"https://openalex.org/W4226298065","doi":"https://doi.org/10.1093/bib/bbac143","title":"On the influence of several factors on pathway enrichment analysis","display_name":"On the influence of several factors on pathway enrichment analysis","publication_year":2022,"publication_date":"2022-04-14","ids":{"openalex":"https://openalex.org/W4226298065","doi":"https://doi.org/10.1093/bib/bbac143","pmid":"https://pubmed.ncbi.nlm.nih.gov/35453140"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac143","pdf_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac143/43745535/bbac143.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac143/43745535/bbac143.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012235619","display_name":"Sarah Mubeen","orcid":"https://orcid.org/0000-0002-9858-3755"},"institutions":[{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sarah Mubeen","raw_affiliation_strings":["Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115 Bonn, Germany","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany","Fraunhofer Center for Machine Learning, Germany"],"affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115 Bonn, Germany","institution_ids":["https://openalex.org/I4210164149","https://openalex.org/I135140700"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Fraunhofer Center for Machine Learning, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000031695","display_name":"Alpha Tom Kodamullil","orcid":"https://orcid.org/0000-0001-9896-3531"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alpha Tom Kodamullil","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003139478","display_name":"Martin Hofmann\u2010Apitius","orcid":"https://orcid.org/0000-0001-9012-6720"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Hofmann-Apitius","raw_affiliation_strings":["Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115 Bonn, Germany","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany"],"affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115 Bonn, Germany","institution_ids":["https://openalex.org/I4210164149","https://openalex.org/I135140700"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043459521","display_name":"Daniel Domingo\u2010Fern\u00e1nd\u00e9z","orcid":"https://orcid.org/0000-0002-2046-6145"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Daniel Domingo-Fern\u00e1ndez","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany","Enveda Biosciences, Boulder, CO, 80301, USA","Fraunhofer Center for Machine Learning, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin 53757, Germany","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Enveda Biosciences, Boulder, CO, 80301, USA","institution_ids":["https://openalex.org/I4210137457"]},{"raw_affiliation_string":"Fraunhofer Center for Machine Learning, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5012235619","https://openalex.org/A5043459521"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210098248","https://openalex.org/I4210137457","https://openalex.org/I4210164149"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":8.9261,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.98785497,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"23","issue":"3","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9876999855041504,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9710999727249146,"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":0.7076012492179871},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7055690884590149},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6490932703018188},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6121312379837036},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.512584388256073},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.47748562693595886},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4305969476699829},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.4194732904434204},{"id":"https://openalex.org/keywords/elegance","display_name":"Elegance","score":0.41506901383399963},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22353410720825195},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.16873329877853394},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.10441836714744568},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07894852757453918}],"concepts":[{"id":"https://openalex.org/C2780586970","wikidata":"https://www.wikidata.org/wiki/Q1357284","display_name":"Popularity","level":2,"score":0.7076012492179871},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7055690884590149},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6490932703018188},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6121312379837036},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.512584388256073},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.47748562693595886},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4305969476699829},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.4194732904434204},{"id":"https://openalex.org/C2778698498","wikidata":"https://www.wikidata.org/wiki/Q1207152","display_name":"Elegance","level":2,"score":0.41506901383399963},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22353410720825195},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.16873329877853394},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.10441836714744568},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07894852757453918},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D005163","descriptor_name":"Factor Analysis, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005163","descriptor_name":"Factor Analysis, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005163","descriptor_name":"Factor Analysis, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008137","descriptor_name":"Longitudinal Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008137","descriptor_name":"Longitudinal Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008137","descriptor_name":"Longitudinal Studies","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbac143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac143","pdf_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac143/43745535/bbac143.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35453140","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35453140","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:bonndoc.ulb.uni-bonn.de:20.500.11811/10617","is_oa":false,"landing_page_url":"https://hdl.handle.net/20.500.11811/10617","pdf_url":null,"source":{"id":"https://openalex.org/S4306402493","display_name":"bonndoc (University of Bonn)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I135140700","host_organization_name":"University of Bonn","host_organization_lineage":["https://openalex.org/I135140700"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doc-type:doctoralThesis"},{"id":"pmh:oai:publica.fraunhofer.de:publica/417645","is_oa":true,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/417645","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":"review"},{"id":"pmh:oai:publica.fraunhofer.de:publica/480995","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/480995","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":"doctoral thesis"},{"id":"pmh:oai:pubmedcentral.nih.gov:9116215","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9116215","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac143","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac143","pdf_url":"https://academic.oup.com/bib/article-pdf/23/3/bbac143/43745535/bbac143.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4226298065.pdf","grobid_xml":"https://content.openalex.org/works/W4226298065.grobid-xml"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W1848567445","https://openalex.org/W1857789879","https://openalex.org/W1968005447","https://openalex.org/W1983463159","https://openalex.org/W1989108446","https://openalex.org/W1989277387","https://openalex.org/W1995329541","https://openalex.org/W2010457001","https://openalex.org/W2011417152","https://openalex.org/W2020859582","https://openalex.org/W2044066230","https://openalex.org/W2063508090","https://openalex.org/W2078284062","https://openalex.org/W2084200259","https://openalex.org/W2084533385","https://openalex.org/W2095900642","https://openalex.org/W2096766502","https://openalex.org/W2100980426","https://openalex.org/W2101536220","https://openalex.org/W2102074241","https://openalex.org/W2102899487","https://openalex.org/W2105734437","https://openalex.org/W2108096229","https://openalex.org/W2110687686","https://openalex.org/W2112220625","https://openalex.org/W2113624587","https://openalex.org/W2118069309","https://openalex.org/W2127401140","https://openalex.org/W2129099812","https://openalex.org/W2130410032","https://openalex.org/W2134736660","https://openalex.org/W2135891958","https://openalex.org/W2139036189","https://openalex.org/W2144766641","https://openalex.org/W2146512944","https://openalex.org/W2148866288","https://openalex.org/W2153848946","https://openalex.org/W2157646380","https://openalex.org/W2158217645","https://openalex.org/W2158384363","https://openalex.org/W2159835316","https://openalex.org/W2165040702","https://openalex.org/W2167119716","https://openalex.org/W2167778120","https://openalex.org/W2183346825","https://openalex.org/W2263356566","https://openalex.org/W2277498598","https://openalex.org/W2517051411","https://openalex.org/W2535702297","https://openalex.org/W2537748973","https://openalex.org/W2560707317","https://openalex.org/W2591941343","https://openalex.org/W2592517962","https://openalex.org/W2749464300","https://openalex.org/W2793555725","https://openalex.org/W2807134042","https://openalex.org/W2891349395","https://openalex.org/W2891585877","https://openalex.org/W2910111050","https://openalex.org/W2912621306","https://openalex.org/W2917858269","https://openalex.org/W2949093503","https://openalex.org/W2950896295","https://openalex.org/W2957376989","https://openalex.org/W2962821542","https://openalex.org/W2964428942","https://openalex.org/W2979832776","https://openalex.org/W2984996233","https://openalex.org/W2989608901","https://openalex.org/W2989619704","https://openalex.org/W3004747635","https://openalex.org/W3039150496","https://openalex.org/W3096828292","https://openalex.org/W3101791085","https://openalex.org/W3102147110","https://openalex.org/W3112600195","https://openalex.org/W3136308181","https://openalex.org/W3153543576","https://openalex.org/W3163048757","https://openalex.org/W3165022492","https://openalex.org/W3196948502","https://openalex.org/W3202651972","https://openalex.org/W4214876469","https://openalex.org/W4226004773","https://openalex.org/W4233698560","https://openalex.org/W4255375128","https://openalex.org/W4297900044","https://openalex.org/W6729009218","https://openalex.org/W6768947953","https://openalex.org/W6779537091","https://openalex.org/W6804504113"],"related_works":["https://openalex.org/W2350726700","https://openalex.org/W2372632584","https://openalex.org/W2391085258","https://openalex.org/W2369724483","https://openalex.org/W2375562526","https://openalex.org/W2387995021","https://openalex.org/W2350229467","https://openalex.org/W4252398414","https://openalex.org/W2352671137","https://openalex.org/W2356937802"],"abstract_inverted_index":{"Pathway":[0],"enrichment":[1,25,35,99,125],"analysis":[2,100],"has":[3,18],"become":[4],"a":[5,90,109,141,153],"widely":[6],"used":[7],"knowledge-based":[8],"approach":[9],"for":[10],"the":[11,31,44,118,134,145,200,214,219],"interpretation":[12],"of":[13,23,33,46,92,111,120,136,147,156,213],"biomedical":[14],"data.":[15],"Its":[16],"popularity":[17],"led":[19],"to":[20,59,67,80,139,162,165,181,190,210],"an":[21,48],"explosion":[22],"both":[24],"methods":[26,69],"and":[27,70,132,173],"pathway":[28,34,124,171],"databases.":[29],"While":[30],"elegance":[32],"lies":[36],"in":[37],"its":[38],"simplicity,":[39],"multiple":[40],"factors":[41,122],"can":[42,188],"impact":[43],"results":[45,85],"such":[47,105,169],"analysis,":[49],"which":[50,216],"may":[51,57],"not":[52],"be":[53,102],"accounted":[54],"for.":[55],"Researchers":[56],"fail":[58],"give":[60],"influential":[61],"aspects":[62,187],"their":[63],"due,":[64],"resorting":[65],"instead":[66],"popular":[68],"gene":[71],"set":[72,82],"collections,":[73],"or":[74,94,193],"default":[75],"settings.":[76],"Despite":[77],"ongoing":[78],"efforts":[79],"establish":[81],"guidelines,":[83],"meaningful":[84],"are":[86],"still":[87],"hampered":[88],"by":[89,202],"lack":[91],"consensus":[93],"gold":[95],"standards":[96],"around":[97],"how":[98,185],"should":[101],"conducted.":[103],"Nonetheless,":[104],"concerns":[106],"have":[107],"prompted":[108],"series":[110],"benchmark":[112],"studies":[113],"specifically":[114],"focused":[115],"on":[116,123,144,184],"evaluating":[117],"influence":[119,146],"various":[121],"results.":[126,196],"In":[127,176],"this":[128],"review,":[129],"we":[130,179,198],"organize":[131],"summarize":[133],"findings":[135],"these":[137,148,186],"benchmarks":[138,205],"provide":[140],"comprehensive":[142],"overview":[143],"factors.":[149,221],"Our":[150],"work":[151],"covers":[152],"broad":[154],"spectrum":[155],"factors,":[157],"spanning":[158],"from":[159,218],"methodological":[160],"assumptions":[161],"those":[163],"related":[164],"prior":[166],"biological":[167],"knowledge,":[168],"as":[170,206,208],"definitions":[172],"database":[174],"choice.":[175],"doing":[177],"so,":[178],"aim":[180],"shed":[182],"light":[183],"lead":[189],"insignificant,":[191],"uninteresting":[192],"even":[194],"contradictory":[195],"Finally,":[197],"conclude":[199],"review":[201],"proposing":[203],"future":[204],"well":[207],"solutions":[209],"overcome":[211],"some":[212],"challenges,":[215],"originate":[217],"outlined":[220]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
