{"id":"https://openalex.org/W2142796008","doi":"https://doi.org/10.1093/bioinformatics/btr142","title":"<i>GO-Module</i>: functional synthesis and improved interpretation of Gene Ontology patterns","display_name":"<i>GO-Module</i>: functional synthesis and improved interpretation of Gene Ontology patterns","publication_year":2011,"publication_date":"2011-03-17","ids":{"openalex":"https://openalex.org/W2142796008","doi":"https://doi.org/10.1093/bioinformatics/btr142","mag":"2142796008","pmid":"https://pubmed.ncbi.nlm.nih.gov/21421553"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr142","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr142","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/10/1444/48861056/bioinformatics_27_10_1444.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/27/10/1444/48861056/bioinformatics_27_10_1444.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079231875","display_name":"Xinan Yang","orcid":"https://orcid.org/0000-0001-8061-8692"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinan Yang","raw_affiliation_strings":["1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100627206","display_name":"Jianrong Li","orcid":"https://orcid.org/0000-0003-2382-6270"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianrong Li","raw_affiliation_strings":["1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100778649","display_name":"Younghee Lee","orcid":"https://orcid.org/0000-0002-6850-0082"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Younghee Lee","raw_affiliation_strings":["1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074706648","display_name":"Yves A. Lussier","orcid":"https://orcid.org/0000-0001-9854-1005"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yves A. Lussier","raw_affiliation_strings":["1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics and 2Comprehensive Cancer Center, Ludwig Center for Metastasis Research, Computation Institute, Institute for Translational Medicine and Institute for Genomics and Systems Biology, the University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5074706648"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5811,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.82885902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"27","issue":"10","first_page":"1444","last_page":"1446"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.49559998512268066,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.49559998512268066,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.46070000529289246,"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":0.007899999618530273,"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/interpretation","display_name":"Interpretation (philosophy)","score":0.7077614068984985},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6362646222114563},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5947489738464355},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.593829870223999},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4730491042137146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4329526424407959},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3611149787902832},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33080804347991943},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23230180144309998},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21038171648979187},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0759223997592926},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.06905195116996765}],"concepts":[{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.7077614068984985},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6362646222114563},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5947489738464355},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.593829870223999},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4730491042137146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4329526424407959},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3611149787902832},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33080804347991943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23230180144309998},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21038171648979187},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0759223997592926},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.06905195116996765},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr142","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr142","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/10/1444/48861056/bioinformatics_27_10_1444.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21421553","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21421553","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/10/1444","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/10/1444","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:pubmedcentral.nih.gov:3087953","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3087953","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr142","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr142","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/10/1444/48861056/bioinformatics_27_10_1444.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2708175070","display_name":null,"funder_award_id":"U54 CA121852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4983833931","display_name":null,"funder_award_id":"UL1 RR024999","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G6673663299","display_name":null,"funder_award_id":"UL1 RR024999-03","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G7583224788","display_name":null,"funder_award_id":"1U54CA121852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7972181056","display_name":null,"funder_award_id":"K22 LM008308","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G8543961968","display_name":null,"funder_award_id":"K22 LM008308-04","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2142796008.pdf","grobid_xml":"https://content.openalex.org/works/W2142796008.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1535641839","https://openalex.org/W1969708590","https://openalex.org/W1999119052","https://openalex.org/W2001560286","https://openalex.org/W2045729458","https://openalex.org/W2072201802","https://openalex.org/W2079577894","https://openalex.org/W2088390270","https://openalex.org/W2094129019","https://openalex.org/W2103017472","https://openalex.org/W2112793962","https://openalex.org/W2122683221","https://openalex.org/W2123318061","https://openalex.org/W2135048780","https://openalex.org/W2138255346","https://openalex.org/W2139084975","https://openalex.org/W2142819802","https://openalex.org/W2144907278","https://openalex.org/W2150392051","https://openalex.org/W2151230991","https://openalex.org/W2152249282","https://openalex.org/W2157033163","https://openalex.org/W2159767718","https://openalex.org/W2166903146"],"related_works":["https://openalex.org/W4313320911","https://openalex.org/W3183204001","https://openalex.org/W4327743144","https://openalex.org/W2607424049","https://openalex.org/W4245077728","https://openalex.org/W4390922876","https://openalex.org/W2185941092","https://openalex.org/W4386782890","https://openalex.org/W3210948575","https://openalex.org/W4206302830"],"abstract_inverted_index":{"UNLABELLED:":[0],"GO-Module":[1,24,72],"is":[2],"a":[3],"web-accessible":[4],"synthesis":[5],"and":[6,52,77],"visualization":[7],"tool":[8],"developed":[9],"for":[10],"end-user":[11],"biologists":[12],"to":[13,61],"greatly":[14],"simplify":[15],"the":[16,27,55,68,84],"interpretation":[17],"of":[18,29,71],"prioritized":[19],"Gene":[20],"Ontology":[21],"(GO)":[22],"terms.":[23],"radically":[25],"reduces":[26],"complexity":[28],"raw":[30],"GO":[31,46,56,86],"results":[32],"into":[33],"compact":[34],"biomodules":[35,43],"in":[36,58],"two":[37],"distinct":[38],"ways,":[39],"by":[40],"(i)":[41],"constructing":[42],"from":[44],"significant":[45],"terms":[47,57,87],"based":[48],"on":[49,78],"hierarchical":[50],"knowledge,":[51],"(ii)":[53],"refining":[54],"each":[59],"biomodule":[60],"contain":[62],"only":[63],"true":[64],"positive":[65],"results.":[66],"Altogether,":[67],"features":[69],"(biomodules)":[70],"outputs":[73],"are":[74],"better":[75],"organized":[76],"average":[79],"four":[80],"times":[81],"smaller":[82],"than":[83],"input":[85],"list":[88],"(P":[89],"=":[90,93],"0.0005,":[91],"n":[92],"16).":[94],"AVAILABILITY:":[95],"http://lussierlab.org/GO-Module.":[96]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2016-06-24T00:00:00"}
