{"id":"https://openalex.org/W3001892728","doi":"https://doi.org/10.1093/bioinformatics/btaa001","title":"GSOAP: a tool for visualization of gene set over-representation analysis","display_name":"GSOAP: a tool for visualization of gene set over-representation analysis","publication_year":2020,"publication_date":"2020-01-21","ids":{"openalex":"https://openalex.org/W3001892728","doi":"https://doi.org/10.1093/bioinformatics/btaa001","mag":"3001892728","pmid":"https://pubmed.ncbi.nlm.nih.gov/31977031"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa001","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2923/33180828/btaa001.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2923/33180828/btaa001.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068185631","display_name":"Tom\u00e1\u0161 Tok\u00e1r","orcid":"https://orcid.org/0000-0002-4873-0032"},"institutions":[{"id":"https://openalex.org/I4210131630","display_name":"Krembil Foundation","ror":"https://ror.org/037svw098","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210131630"]},{"id":"https://openalex.org/I4388446386","display_name":"Krembil Research Institute","ror":"https://ror.org/01f6jys10","country_code":null,"type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Tomas Tokar","raw_affiliation_strings":["Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada"],"raw_orcid":"https://orcid.org/0000-0002-4873-0032","affiliations":[{"raw_affiliation_string":"Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada","institution_ids":["https://openalex.org/I4210131630","https://openalex.org/I4388446386"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085732287","display_name":"Chiara Pastrello","orcid":"https://orcid.org/0000-0002-1934-7472"},"institutions":[{"id":"https://openalex.org/I4210131630","display_name":"Krembil Foundation","ror":"https://ror.org/037svw098","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210131630"]},{"id":"https://openalex.org/I4388446386","display_name":"Krembil Research Institute","ror":"https://ror.org/01f6jys10","country_code":null,"type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chiara Pastrello","raw_affiliation_strings":["Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada","institution_ids":["https://openalex.org/I4210131630","https://openalex.org/I4388446386"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055656807","display_name":"Igor Juri\u0161ica","orcid":"https://orcid.org/0000-0002-2507-946X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I207624831","display_name":"Slovak Academy of Sciences","ror":"https://ror.org/03h7qq074","country_code":"SK","type":"government","lineage":["https://openalex.org/I207624831"]},{"id":"https://openalex.org/I4210131630","display_name":"Krembil Foundation","ror":"https://ror.org/037svw098","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210131630"]},{"id":"https://openalex.org/I4210145572","display_name":"Institute of Neuroimmunology of the Slovak Academy of Sciences","ror":"https://ror.org/05c516317","country_code":"SK","type":"facility","lineage":["https://openalex.org/I207624831","https://openalex.org/I4210145572"]},{"id":"https://openalex.org/I4388446386","display_name":"Krembil Research Institute","ror":"https://ror.org/01f6jys10","country_code":null,"type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386"]}],"countries":["CA","SK"],"is_corresponding":true,"raw_author_name":"Igor Jurisica","raw_affiliation_strings":["Department of Computer Science , University of Toronto, Toronto, ON M5T 3A1, Canada","Department of Medical Biophysics , University of Toronto, Toronto, ON M5G 1L7, Canada","Institute of Neuroimmunology , Slovak Academy of Sciences, Dubravska cesta 9, SK-84510, Bratislava, Slovakia","Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of Toronto, Toronto, ON M5T 3A1, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Medical Biophysics , University of Toronto, Toronto, ON M5G 1L7, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Institute of Neuroimmunology , Slovak Academy of Sciences, Dubravska cesta 9, SK-84510, Bratislava, Slovakia","institution_ids":["https://openalex.org/I207624831","https://openalex.org/I4210145572"]},{"raw_affiliation_string":"Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada","institution_ids":["https://openalex.org/I4210131630","https://openalex.org/I4388446386"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5055656807"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I207624831","https://openalex.org/I4210131630","https://openalex.org/I4210145572","https://openalex.org/I4388446386"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.0603,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.74314657,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"9","first_page":"2923","last_page":"2925"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8567000031471252,"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":0.8567000031471252,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.04910000041127205,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.0364999994635582,"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/visualization","display_name":"Visualization","score":0.7734857797622681},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.716697096824646},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.664969801902771},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5872192978858948},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4101668894290924},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26155078411102295},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21753552556037903},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18452715873718262}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7734857797622681},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.716697096824646},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.664969801902771},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5872192978858948},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4101668894290924},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26155078411102295},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21753552556037903},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18452715873718262},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa001","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2923/33180828/btaa001.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31977031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31977031","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7203738","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7203738","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa001","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2923/33180828/btaa001.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2153463635","display_name":null,"funder_award_id":"225404","funder_id":"https://openalex.org/F4320310293","funder_display_name":"Cummings Foundation"},{"id":"https://openalex.org/G316236377","display_name":null,"funder_award_id":"30865","funder_id":"https://openalex.org/F4320310293","funder_display_name":"Cummings Foundation"},{"id":"https://openalex.org/G5639122495","display_name":null,"funder_award_id":"203475","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320310293","display_name":"Cummings Foundation","ror":"https://ror.org/01vkhxt72"},{"id":"https://openalex.org/F4320319952","display_name":"Canada Foundation for Innovation","ror":"https://ror.org/000az4664"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3001892728.pdf","grobid_xml":"https://content.openalex.org/works/W3001892728.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1975434639","https://openalex.org/W2001141328","https://openalex.org/W2035618305","https://openalex.org/W2067752346","https://openalex.org/W2145496876","https://openalex.org/W2169507824","https://openalex.org/W2187089797","https://openalex.org/W2558585189","https://openalex.org/W2782759066"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2068608913","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3124914020","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1],"sets":[2],"over-representation":[3],"analysis":[4,12],"(GSOA)":[5],"is":[6,30,75,82],"a":[7,18,44],"common":[8],"technique":[9],"of":[10,37,47],"enrichment":[11],"that":[13],"measures":[14],"the":[15,48,53,56],"overlap":[16],"between":[17],"gene":[19],"set":[20],"and":[21,69,81],"selected":[22],"instances":[23],"(e.g.":[24],"pathways).":[25],"Despite":[26],"its":[27],"popularity,":[28],"there":[29],"currently":[31],"no":[32],"established":[33],"standard":[34],"for":[35],"visualization":[36],"GSOA":[38,49],"results.":[39],"RESULTS:":[40],"Here,":[41],"we":[42],"propose":[43],"visual":[45],"exploration":[46],"results":[50],"by":[51],"showing":[52],"relationships":[54],"among":[55],"enriched":[57],"instances,":[58],"while":[59],"highlighting":[60],"important":[61],"instance":[62],"attributes,":[63],"such":[64],"as":[65,77],"significance,":[66],"closeness":[67],"(centrality)":[68],"clustering.":[70],"AVAILABILITY":[71],"AND":[72],"IMPLEMENTATION:":[73],"GSOAP":[74],"implemented":[76],"an":[78],"R":[79],"package":[80],"available":[83],"at":[84],"https://github.com/tomastokar/gsoap.":[85]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":1}],"updated_date":"2026-09-11T09:22:31.653822","created_date":"2025-10-10T00:00:00"}
