{"id":"https://openalex.org/W1994784108","doi":"https://doi.org/10.1109/tcbb.2014.2385702","title":"Building Transcriptional Association Networks in Cytoscape with RegNetC","display_name":"Building Transcriptional Association Networks in Cytoscape with RegNetC","publication_year":2014,"publication_date":"2014-12-23","ids":{"openalex":"https://openalex.org/W1994784108","doi":"https://doi.org/10.1109/tcbb.2014.2385702","mag":"1994784108","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357322"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2385702","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2385702","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/11441/133495","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018933874","display_name":"Isabel A. Nepomuceno-Chamorro","orcid":"https://orcid.org/0000-0002-4255-7160"},"institutions":[{"id":"https://openalex.org/I79238269","display_name":"Universidad de Sevilla","ror":"https://ror.org/03yxnpp24","country_code":"ES","type":"education","lineage":["https://openalex.org/I79238269"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Isabel A. Nepomuceno-Chamorro","raw_affiliation_strings":["Department of Lenguajes y Sistemas Informaticos, Universidad de Sevilla, Spain","[Department of Lenguajes y Sistemas Informaticos, Universidad de Sevilla, Spain]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Lenguajes y Sistemas Informaticos, Universidad de Sevilla, Spain","institution_ids":["https://openalex.org/I79238269"]},{"raw_affiliation_string":"[Department of Lenguajes y Sistemas Informaticos, Universidad de Sevilla, Spain]","institution_ids":["https://openalex.org/I79238269"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055088215","display_name":"Alfonso E. M\u00e1rquez-Chamorro","orcid":"https://orcid.org/0000-0002-8243-0404"},"institutions":[{"id":"https://openalex.org/I95013407","display_name":"Universidad Pablo de Olavide","ror":"https://ror.org/02z749649","country_code":"ES","type":"education","lineage":["https://openalex.org/I95013407"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alfonso Marquez-Chamorro","raw_affiliation_strings":["School of Engineering, Pablo de Olavide University, Seville, Spain","School of Engineering, Pablo de Olavide University, Seville, Spain#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering, Pablo de Olavide University, Seville, Spain","institution_ids":["https://openalex.org/I95013407"]},{"raw_affiliation_string":"School of Engineering, Pablo de Olavide University, Seville, Spain#TAB#","institution_ids":["https://openalex.org/I95013407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049817649","display_name":"Jes\u00fas S. Aguilar\u2013Ruiz","orcid":"https://orcid.org/0000-0002-2666-293X"},"institutions":[{"id":"https://openalex.org/I95013407","display_name":"Universidad Pablo de Olavide","ror":"https://ror.org/02z749649","country_code":"ES","type":"education","lineage":["https://openalex.org/I95013407"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jesus S. Aguilar-Ruiz","raw_affiliation_strings":["School of Engineering, Pablo de Olavide University, Seville, Spain","School of Engineering, Pablo de Olavide University, Seville, Spain#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering, Pablo de Olavide University, Seville, Spain","institution_ids":["https://openalex.org/I95013407"]},{"raw_affiliation_string":"School of Engineering, Pablo de Olavide University, Seville, Spain#TAB#","institution_ids":["https://openalex.org/I95013407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.05719573,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"4","first_page":"823","last_page":"824"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9994000196456909,"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":0.989799976348877,"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/plug-in","display_name":"Plug-in","score":0.7886137962341309},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5405752658843994},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.49336114525794983},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4844065308570862},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4825822412967682},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.47791725397109985},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.4626980423927307},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44929611682891846},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.44411057233810425},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4412161111831665},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41342395544052124},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30978626012802124},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2909751832485199},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2515450119972229},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.20477113127708435},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18893611431121826},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14328798651695251},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.099689781665802}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.7886137962341309},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5405752658843994},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.49336114525794983},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4844065308570862},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4825822412967682},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.47791725397109985},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.4626980423927307},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44929611682891846},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44411057233810425},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4412161111831665},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41342395544052124},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30978626012802124},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2909751832485199},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2515450119972229},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.20477113127708435},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18893611431121826},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14328798651695251},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.099689781665802},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"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":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2014.2385702","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2385702","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26357322","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357322","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:idus.us.es:11441/133495","is_oa":true,"landing_page_url":"https://hdl.handle.net/11441/133495","pdf_url":null,"source":{"id":"https://openalex.org/S4306401665","display_name":"Deposito de Investigacion Universidad de Sevilla (University of Seville)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79238269","host_organization_name":"Universidad de Sevilla","host_organization_lineage":["https://openalex.org/I79238269"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"}],"best_oa_location":{"id":"pmh:oai:idus.us.es:11441/133495","is_oa":true,"landing_page_url":"https://hdl.handle.net/11441/133495","pdf_url":null,"source":{"id":"https://openalex.org/S4306401665","display_name":"Deposito de Investigacion Universidad de Sevilla (University of Seville)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79238269","host_organization_name":"Universidad de Sevilla","host_organization_lineage":["https://openalex.org/I79238269"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1570448133","https://openalex.org/W1596515083","https://openalex.org/W2000860171","https://openalex.org/W2005889734","https://openalex.org/W2030455922","https://openalex.org/W2103017472","https://openalex.org/W2109969031","https://openalex.org/W2110336313","https://openalex.org/W2112473584","https://openalex.org/W2115108153","https://openalex.org/W2125698969","https://openalex.org/W2133990480","https://openalex.org/W2158217645","https://openalex.org/W2159675211","https://openalex.org/W2169950095","https://openalex.org/W2966207845"],"related_works":["https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W47352601","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W4231704780","https://openalex.org/W631546281","https://openalex.org/W2266220644","https://openalex.org/W88292646"],"abstract_inverted_index":{"The":[0],"Regression":[1],"Network":[2],"plugin":[3,99,146],"for":[4,11,123,136],"Cytoscape":[5,98,130],"(RegNetC)":[6],"implements":[7],"the":[8,12,31,37,62,81,114,142,144,149,161,168],"RegNet":[9],"algorithm":[10,23],"inference":[13],"of":[14,42,47,80,84,156],"transcriptional":[15,116],"association":[16,118],"network":[17,119],"from":[18],"gene":[19,35,63,117],"expression":[20,64,154],"profiles.":[21],"This":[22],"is":[24,78],"a":[25,56,97],"model":[26],"tree-based":[27],"method":[28],"to":[29,60,111,141],"detect":[30],"relationship":[32],"between":[33,152],"each":[34,45],"and":[36,69,126],"remaining":[38],"genes":[39,48,153,158],"simultaneously":[40],"instead":[41],"analyzing":[43],"individually":[44],"pair":[46],"as":[49,96,106],"correlation-based":[50,85],"methods":[51],"do.":[52],"Model":[53],"trees":[54],"are":[55],"very":[57],"useful":[58],"technique":[59],"estimate":[61],"value":[65],"by":[66,167],"regression":[67,169],"models":[68],"favours":[70],"localized":[71],"similarities":[72],"over":[73],"more":[74],"global":[75],"similarity,":[76],"which":[77,132],"one":[79],"major":[82],"drawbacks":[83],"methods.":[86],"Here,":[87],"we":[88],"present":[89],"an":[90],"integrated":[91],"software":[92],"suite,":[93],"named":[94],"RegNetC,":[95],"that":[100],"can":[101,133],"operate":[102],"on":[103],"its":[104],"own":[105],"well.":[107],"RegNetC":[108,145],"facilitates,":[109],"according":[110],"user-defined":[112],"parameters,":[113],"resulted":[115],"in":[120,160],".sif":[121],"format":[122],"visualization,":[124],"analysis":[125],"interoperates":[127],"with":[128],"other":[129],"plugins,":[131],"be":[134],"exported":[135],"publication":[137],"figures.":[138],"In":[139],"addition":[140],"network,":[143,163],"also":[147],"provides":[148],"quantitative":[150],"relationships":[151],"values":[155],"those":[157,165],"involved":[159],"inferred":[162],"i.e.,":[164],"defined":[166],"models.":[170]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
