{"id":"https://openalex.org/W2162501402","doi":"https://doi.org/10.1093/bioinformatics/bts041","title":"CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores","display_name":"CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores","publication_year":2012,"publication_date":"2012-02-15","ids":{"openalex":"https://openalex.org/W2162501402","doi":"https://doi.org/10.1093/bioinformatics/bts041","mag":"2162501402","pmid":"https://pubmed.ncbi.nlm.nih.gov/22345616"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts041","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/893/48880506/bioinformatics_28_6_893.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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/893/48880506/bioinformatics_28_6_893.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088040720","display_name":"Aleksandar Stojmirovi\u0107","orcid":"https://orcid.org/0000-0003-0957-6893"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aleksandar Stojmirovi\u0107","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016352006","display_name":"Alexander Bliskovsky","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Bliskovsky","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080970152","display_name":"Yi\u2010Kuo Yu","orcid":"https://orcid.org/0000-0002-6213-7665"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yi-Kuo Yu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080970152"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.403,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.6336779,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"28","issue":"6","first_page":"893","last_page":"894"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9965000152587891,"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":0.9965000152587891,"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":0.965399980545044,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9387000203132629,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7814773917198181},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.755854606628418},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.747946560382843},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.5084637403488159},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.45146727561950684},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.4160422682762146},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3874641954898834},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20901745557785034},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1685749888420105}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7814773917198181},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.755854606628418},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.747946560382843},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.5084637403488159},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.45146727561950684},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4160422682762146},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3874641954898834},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20901745557785034},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1685749888420105},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":"D009317","descriptor_name":"National Library of Medicine (U.S.)","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009317","descriptor_name":"National Library of Medicine (U.S.)","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009317","descriptor_name":"National Library of Medicine (U.S.)","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":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts041","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/893/48880506/bioinformatics_28_6_893.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:22345616","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22345616","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:pubmedcentral.nih.gov:3307116","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3307116","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:arXiv.org:1110.5006","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1110.5006","pdf_url":"https://arxiv.org/pdf/1110.5006","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts041","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/893/48880506/bioinformatics_28_6_893.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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1236321187","https://openalex.org/W2107580398","https://openalex.org/W2123060905","https://openalex.org/W2130410032","https://openalex.org/W2155142785","https://openalex.org/W2170937146","https://openalex.org/W2331747324","https://openalex.org/W4237381349","https://openalex.org/W4254695622"],"related_works":["https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W631546281","https://openalex.org/W4206501676","https://openalex.org/W88292646","https://openalex.org/W2266220644"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"CytoSaddleSum":[2],"provides":[3],"Cytoscape":[4,67],"users":[5],"with":[6],"access":[7],"to":[8,37],"the":[9,28],"functionality":[10],"of":[11],"SaddleSum,":[12],"a":[13,38,48],"functional":[14,42],"enrichment":[15,43],"tool":[16],"based":[17],"on":[18],"sum-of-weight":[19],"scores.":[20],"It":[21],"operates":[22],"by":[23],"querying":[24],"SaddleSum":[25],"locally":[26],"(using":[27],"standalone":[29],"version)":[30],"or":[31],"remotely":[32],"(through":[33],"an":[34],"HTTP":[35],"request":[36],"web":[39],"server).":[40],"The":[41,82],"results":[44,63],"are":[45,64,96],"shown":[46],"as":[47,66],"term":[49,59],"relationship":[50],"network,":[51],"where":[52],"nodes":[53],"represent":[54],"terms":[55],"and":[56,73],"edges":[57],"show":[58],"relationships.":[60],"Furthermore,":[61],"query":[62],"written":[65],"attributes":[68],"allowing":[69],"easy":[70],"saving,":[71],"retrieval":[72],"integration":[74],"into":[75],"network-based":[76],"data":[77],"analysis":[78],"workflows.":[79],"Availability:":[80],"www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html":[81],"source":[83],"code":[84],"is":[85],"placed":[86],"in":[87],"Public":[88],"Domain.":[89],"Contact:":[90],"yyu@ncbi.nlm.nih.gov":[91],"Supplementary":[92,94],"information:":[93],"materials":[95],"available":[97],"at":[98],"Bioinformatics":[99],"online.":[100]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
