{"id":"https://openalex.org/W2027895157","doi":"https://doi.org/10.1093/bib/bbr049","title":"Gene set enrichment analysis: performance evaluation and usage guidelines","display_name":"Gene set enrichment analysis: performance evaluation and usage guidelines","publication_year":2011,"publication_date":"2011-09-07","ids":{"openalex":"https://openalex.org/W2027895157","doi":"https://doi.org/10.1093/bib/bbr049","mag":"2027895157","pmid":"https://pubmed.ncbi.nlm.nih.gov/21900207"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr049","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/281/678618/bbr049.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/13/3/281/678618/bbr049.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025474727","display_name":"Jui\u2010Hung Hung","orcid":"https://orcid.org/0000-0003-2208-9213"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"J.-H. Hung","raw_affiliation_strings":["Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028273823","display_name":"Tzu-Hsien Yang","orcid":"https://orcid.org/0000-0001-9420-196X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T.-H. Yang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023532909","display_name":"Z. Hu","orcid":"https://orcid.org/0000-0001-9665-2609"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Z. Hu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084369008","display_name":"Zhiping Weng","orcid":"https://orcid.org/0000-0002-3032-7966"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Z. Weng","raw_affiliation_strings":["University of Massachusetts Medical School"],"affiliations":[{"raw_affiliation_string":"University of Massachusetts Medical School","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027378666","display_name":"Charles DeLisi","orcid":"https://orcid.org/0000-0002-5847-1599"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C. DeLisi","raw_affiliation_strings":["Boston University"],"affiliations":[{"raw_affiliation_string":"Boston University","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5025474727"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.2702,"has_fulltext":false,"cited_by_count":284,"citation_normalized_percentile":{"value":0.97409652,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"13","issue":"3","first_page":"281","last_page":"291"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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":0.9991000294685364,"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":0.996999979019165,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9778000116348267,"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/voting","display_name":"Voting","score":0.6501768827438354},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5659552812576294},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5506913661956787},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5325573682785034},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4524022042751312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3925285339355469},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2611796259880066}],"concepts":[{"id":"https://openalex.org/C520049643","wikidata":"https://www.wikidata.org/wiki/Q189760","display_name":"Voting","level":3,"score":0.6501768827438354},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5659552812576294},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5506913661956787},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5325573682785034},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4524022042751312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3925285339355469},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2611796259880066},{"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"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":"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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbr049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr049","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/281/678618/bbr049.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21900207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21900207","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:escholarship.umassmed.edu:bioinformatics_pubs-1021","is_oa":false,"landing_page_url":"https://escholarship.umassmed.edu/bioinformatics_pubs/22","pdf_url":null,"source":{"id":"https://openalex.org/S4306400883","display_name":"The Journal of the American Medical Association (JAMA) Network (American Medical Association)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173654999","host_organization_name":"American Medical Association","host_organization_lineage":["https://openalex.org/I173654999"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Program in Bioinformatics and Integrative Biology Publications","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2638327","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3357488","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3357488","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3357488","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbr049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr049","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/281/678618/bbr049.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6000000238418579,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2027895157.pdf","grobid_xml":"https://content.openalex.org/works/W2027895157.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1483505747","https://openalex.org/W1533179050","https://openalex.org/W1563388055","https://openalex.org/W1629615361","https://openalex.org/W1964895626","https://openalex.org/W1973831834","https://openalex.org/W1976050474","https://openalex.org/W1983463159","https://openalex.org/W2011696346","https://openalex.org/W2018407943","https://openalex.org/W2020859582","https://openalex.org/W2031818334","https://openalex.org/W2032850607","https://openalex.org/W2051102111","https://openalex.org/W2077631777","https://openalex.org/W2078284062","https://openalex.org/W2082081674","https://openalex.org/W2086258274","https://openalex.org/W2100639130","https://openalex.org/W2102074241","https://openalex.org/W2103209361","https://openalex.org/W2105022693","https://openalex.org/W2107564978","https://openalex.org/W2109972881","https://openalex.org/W2110065044","https://openalex.org/W2110687686","https://openalex.org/W2111104102","https://openalex.org/W2113533151","https://openalex.org/W2125905177","https://openalex.org/W2128215982","https://openalex.org/W2130410032","https://openalex.org/W2130666470","https://openalex.org/W2131046448","https://openalex.org/W2131657764","https://openalex.org/W2133465414","https://openalex.org/W2133579817","https://openalex.org/W2135230352","https://openalex.org/W2135445066","https://openalex.org/W2138133187","https://openalex.org/W2139036189","https://openalex.org/W2141703917","https://openalex.org/W2144983644","https://openalex.org/W2145025818","https://openalex.org/W2146076957","https://openalex.org/W2146565683","https://openalex.org/W2148139839","https://openalex.org/W2153452513","https://openalex.org/W2154431984","https://openalex.org/W2154972152","https://openalex.org/W2162342992","https://openalex.org/W2167119716","https://openalex.org/W2167809864","https://openalex.org/W2170989872","https://openalex.org/W4230812994"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802","https://openalex.org/W4234157524"],"abstract_inverted_index":{"A":[0],"central":[1],"goal":[2],"of":[3,12,16,43,47,92,103,130,138,145],"biology":[4],"is":[5,73],"understanding":[6],"and":[7,24,28,83,121],"describing":[8],"the":[9,14,29,32,58,84,128,143],"molecular":[10],"basis":[11],"plasticity:":[13],"sets":[15,46,141],"genes":[17,48,56],"that":[18],"are":[19,49,61,77],"combinatorially":[20],"selected":[21],"by":[22,51],"exogenous":[23],"endogenous":[25],"environmental":[26],"changes,":[27],"relations":[30],"among":[31,63],"genes.":[33],"The":[34],"most":[35,74],"viable":[36],"current":[37],"approach":[38],"to":[39,70,80],"this":[40,81],"problem":[41],"consists":[42],"determining":[44],"whether":[45],"connected":[50],"some":[52],"common":[53,100],"theme,":[54],"e.g.":[55],"from":[57],"same":[59],"pathway":[60],"overrepresented":[62],"those":[64],"whose":[65],"differential":[66],"expression":[67],"in":[68,142],"response":[69],"a":[71,89,99,104,123,135,146],"perturbation":[72],"pronounced.":[75],"There":[76],"many":[78],"approaches":[79],"problem,":[82],"results":[85],"they":[86,95],"produce":[87],"show":[88],"fair":[90],"amount":[91],"dispersion,":[93],"but":[94],"all":[96],"fall":[97],"within":[98],"framework":[101],"consisting":[102],"few":[105],"basic":[106],"components.":[107],"We":[108],"critically":[109],"review":[110],"these":[111],"components,":[112],"suggest":[113],"best":[114],"practices":[115],"for":[116,126],"carrying":[117],"out":[118],"each":[119],"step,":[120],"propose":[122],"voting":[124],"method":[125],"meeting":[127],"challenge":[129],"assessing":[131],"different":[132],"methods":[133],"on":[134],"large":[136],"number":[137],"experimental":[139],"data":[140],"absence":[144],"gold":[147],"standard.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":36},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":21},{"year":2014,"cited_by_count":21},{"year":2013,"cited_by_count":16},{"year":2012,"cited_by_count":10}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
