{"id":"https://openalex.org/W2281247410","doi":"https://doi.org/10.1093/bib/bbv091","title":"Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls","display_name":"Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls","publication_year":2015,"publication_date":"2015-10-07","ids":{"openalex":"https://openalex.org/W2281247410","doi":"https://doi.org/10.1093/bib/bbv091","mag":"2281247410","pmid":"https://pubmed.ncbi.nlm.nih.gov/26446060"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv091","pdf_url":"https://academic.oup.com/bib/article-pdf/17/5/808/17485780/bbv091.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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/17/5/808/17485780/bbv091.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032694209","display_name":"Rosa J. Meijer","orcid":null},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Rosa J. Meijer","raw_affiliation_strings":["Rosa J. Meijer is statistical consultant at Statistics Netherlands. This work is part of her PhD research at the Department of Medical Statistics and Bioinformatics at Leiden University Medical Center, which focused on structured multiple testing problems"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosa J. Meijer is statistical consultant at Statistics Netherlands. This work is part of her PhD research at the Department of Medical Statistics and Bioinformatics at Leiden University Medical Center, which focused on structured multiple testing problems","institution_ids":["https://openalex.org/I2800006345"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032056430","display_name":"Jelle J. Goeman","orcid":"https://orcid.org/0000-0003-4283-0259"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jelle J. Goeman","raw_affiliation_strings":["Jelle J. Goeman is professor of Biostatistics at Radboud University Medical Center in Nijmegen. His research focuses on high-dimensional data, prediction modeling, hypothesis testing and multiple testing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jelle J. Goeman is professor of Biostatistics at Radboud University Medical Center in Nijmegen. His research focuses on high-dimensional data, prediction modeling, hypothesis testing and multiple testing","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802934949"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":0.6937,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.70688369,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"5","first_page":"808","last_page":"818"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.998199999332428,"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":0.998199999332428,"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":0.996399998664856,"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/T11235","display_name":"Statistical Methods in Clinical Trials","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.7566077709197998},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7492871880531311},{"id":"https://openalex.org/keywords/multiple-comparisons-problem","display_name":"Multiple comparisons problem","score":0.6806800365447998},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5759404301643372},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5497168302536011},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5497142672538757},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.5236698985099792},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45064952969551086},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.42108821868896484},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.41005152463912964},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28054630756378174},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.216263085603714},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17752927541732788},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14507490396499634},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09042057394981384},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0844162106513977},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07690063118934631}],"concepts":[{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.7566077709197998},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7492871880531311},{"id":"https://openalex.org/C183905921","wikidata":"https://www.wikidata.org/wiki/Q1038757","display_name":"Multiple comparisons problem","level":2,"score":0.6806800365447998},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5759404301643372},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5497168302536011},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5497142672538757},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.5236698985099792},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45064952969551086},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.42108821868896484},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.41005152463912964},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28054630756378174},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.216263085603714},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17752927541732788},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14507490396499634},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09042057394981384},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0844162106513977},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07690063118934631},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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}],"mesh":[{"descriptor_ui":"D005820","descriptor_name":"Genetic Testing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005820","descriptor_name":"Genetic Testing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005820","descriptor_name":"Genetic Testing","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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbv091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv091","pdf_url":"https://academic.oup.com/bib/article-pdf/17/5/808/17485780/bbv091.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:26446060","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26446060","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":"Journal Article"},{"id":"pmh:lumc:oai:scholarlypublications.universiteitleiden.nl:item_2998850","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/113023","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 17(5), 808 - 818","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/5/808","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/5/808","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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:repository.ubn.ru.nl:2066/171010","is_oa":false,"landing_page_url":"http://hdl.handle.net/2066/171010","pdf_url":null,"source":{"id":"https://openalex.org/S4306401067","display_name":"Radboud Repository (Radboud University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145872427","host_organization_name":"Radboud University Nijmegen","host_organization_lineage":["https://openalex.org/I145872427"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 17, 5, pp. 808-18","raw_type":"Article / Letter to editor"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_2998850","is_oa":false,"landing_page_url":"https://hdl.handle.net/1887/113023","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv091","pdf_url":"https://academic.oup.com/bib/article-pdf/17/5/808/17485780/bbv091.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":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2281247410.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1576695541","https://openalex.org/W1596515083","https://openalex.org/W1637271240","https://openalex.org/W1805085228","https://openalex.org/W1973024816","https://openalex.org/W1974530346","https://openalex.org/W1986589809","https://openalex.org/W2021880490","https://openalex.org/W2022234808","https://openalex.org/W2025126377","https://openalex.org/W2035923145","https://openalex.org/W2036714085","https://openalex.org/W2059501425","https://openalex.org/W2088160256","https://openalex.org/W2099657218","https://openalex.org/W2101536220","https://openalex.org/W2103017472","https://openalex.org/W2105022693","https://openalex.org/W2110065044","https://openalex.org/W2115012618","https://openalex.org/W2118069309","https://openalex.org/W2120024428","https://openalex.org/W2121044470","https://openalex.org/W2122084873","https://openalex.org/W2134736660","https://openalex.org/W2135230352","https://openalex.org/W2138255346","https://openalex.org/W2141703917","https://openalex.org/W2144907278","https://openalex.org/W2163563958","https://openalex.org/W2165476567","https://openalex.org/W2606759007","https://openalex.org/W2796856748","https://openalex.org/W3099580112","https://openalex.org/W4230741409","https://openalex.org/W6678230397"],"related_works":["https://openalex.org/W4293336298","https://openalex.org/W2467227750","https://openalex.org/W2093104131","https://openalex.org/W2178204436","https://openalex.org/W4300887971","https://openalex.org/W2143079975","https://openalex.org/W2333750400","https://openalex.org/W1986765826","https://openalex.org/W2766832551","https://openalex.org/W1921844237"],"abstract_inverted_index":{"The":[0],"use":[1],"of":[2,9,71,93,101,117,127],"multiple":[3,21,73],"testing":[4,11,22,74],"procedures":[5,75],"in":[6,42,137],"the":[7,44,50,82,91,99,128,138],"context":[8],"gene-set":[10],"is":[12,24,27],"an":[13,115],"important":[14],"but":[15],"relatively":[16],"underexposed":[17],"topic.":[18],"If":[19],"a":[20,29,118,124],"method":[23,130],"used,":[25],"this":[26],"usually":[28],"standard":[30],"familywise":[31],"error":[32],"rate":[33,38],"(FWER)":[34],"or":[35],"false":[36],"discovery":[37],"(FDR)":[39],"controlling":[40,105,112],"procedure":[41],"which":[43,133],"logical":[45],"relationships":[46,61],"that":[47],"exist":[48],"between":[49],"different":[51],"(self-contained)":[52],"hypotheses":[53],"are":[54,107],"not":[55],"taken":[56],"into":[57,62],"account.":[58],"Taking":[59],"those":[60],"account,":[63],"however,":[64],"can":[65,77],"lead":[66],"to":[67],"more":[68,108],"powerful":[69],"variants":[70],"existing":[72],"and":[76,80],"make":[78],"summarizing":[79],"interpreting":[81],"final":[83],"results":[84],"easier.":[85],"We":[86],"will":[87],"show":[88],"that,":[89],"from":[90,98],"perspective":[92,100],"interpretation":[94],"as":[95,97],"well":[96],"power":[102,120],"improvement,":[103,121],"FWER":[104],"methods":[106],"suitable":[109],"than":[110],"FDR":[111],"methods.":[113],"As":[114],"example":[116],"possible":[119],"we":[122,134],"suggest":[123],"modified":[125],"version":[126],"popular":[129],"by":[131],"Holm,":[132],"also":[135],"implemented":[136],"R":[139],"package":[140],"cherry.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3}],"updated_date":"2026-08-31T07:19:18.363097","created_date":"2025-10-10T00:00:00"}
