{"id":"https://openalex.org/W2156431842","doi":"https://doi.org/10.1186/1752-0509-8-s4-s2","title":"TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles","display_name":"TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2156431842","doi":"https://doi.org/10.1186/1752-0509-8-s4-s2","mag":"2156431842","pmid":"https://pubmed.ncbi.nlm.nih.gov/25522063"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-8-s4-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s4-s2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005993955","display_name":"Ashwini Patil","orcid":"https://orcid.org/0000-0002-3353-1970"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ashwini Patil","raw_affiliation_strings":["Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054681585","display_name":"Kenta Nakai","orcid":"https://orcid.org/0000-0002-8721-8883"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenta Nakai","raw_affiliation_strings":["Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005993955"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":null,"apc_paid":null,"fwci":0.7114,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.71003742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"8","issue":"Suppl 4","first_page":"S2","last_page":"S2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9643999934196472,"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":0.9643999934196472,"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":0.018300000578165054,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0020000000949949026,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.671216607093811},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.627084493637085},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6024976968765259},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6022427678108215},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5280776023864746},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4933389723300934},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4870770275592804},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4863179624080658},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.434822678565979},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3227198123931885}],"concepts":[{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.671216607093811},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.627084493637085},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6024976968765259},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6022427678108215},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5280776023864746},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4933389723300934},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4870770275592804},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4863179624080658},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.434822678565979},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3227198123931885}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007113","descriptor_name":"Immunity, Innate","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007113","descriptor_name":"Immunity, Innate","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007113","descriptor_name":"Immunity, Innate","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009997","descriptor_name":"Osmotic Pressure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009997","descriptor_name":"Osmotic Pressure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009997","descriptor_name":"Osmotic Pressure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-8-s4-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s4-s2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:25522063","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25522063","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4290689","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4290689","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-8-s4-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s4-s2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S4-S2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320336716","display_name":"Institute of Medical Science, University of Tokyo","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2156431842.pdf","grobid_xml":"https://content.openalex.org/works/W2156431842.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1918391659","https://openalex.org/W1998767819","https://openalex.org/W2000860171","https://openalex.org/W2007222211","https://openalex.org/W2052685738","https://openalex.org/W2069645361","https://openalex.org/W2072009200","https://openalex.org/W2089691349","https://openalex.org/W2102265464","https://openalex.org/W2120889962","https://openalex.org/W2129265876","https://openalex.org/W2135030836","https://openalex.org/W2136303131","https://openalex.org/W2136910340","https://openalex.org/W2141152663","https://openalex.org/W2144738674","https://openalex.org/W2147735312","https://openalex.org/W2160756584"],"related_works":["https://openalex.org/W2052655934","https://openalex.org/W2949927938","https://openalex.org/W2029387041","https://openalex.org/W104645380","https://openalex.org/W2135896045","https://openalex.org/W2010571965","https://openalex.org/W2027213253","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2023641020"],"abstract_inverted_index":{"BACKGROUND:":[0],"Time-course":[1],"gene":[2,57,61,73,80,89,142,236],"expression":[3,62,81,119],"profiles":[4,82],"are":[5,49],"frequently":[6],"used":[7,223],"to":[8,20,44,52,106,132,157,164,187,198,224,228],"provide":[9,36],"insight":[10],"into":[11],"the":[12,22,39,84,101,108,113,145,151,202,210,231],"changes":[13,117],"in":[14,83,118,144,201,209,238,253,275],"cellular":[15,42,226],"state":[16],"over":[17],"time":[18,122],"and":[19,91,136,150,259,265],"infer":[21],"molecular":[23,30,211],"pathways":[24,139,182],"involved.":[25],"When":[26],"combined":[27],"with":[28,75,115,183],"large-scale":[29],"interaction":[31,93,212],"networks,":[32],"such":[33],"data":[34],"can":[35,221,271],"information":[37],"about":[38],"dynamics":[40],"of":[41,86,100,180,204,207,233,269],"response":[43,149,227],"stimulus.":[45],"However,":[46],"few":[47],"tools":[48],"currently":[50],"available":[51,280],"predict":[53,133],"a":[54,67,87,97,177,217,256],"single":[55],"active":[56,72,141,235],"sub-network":[58],"from":[59,169],"time-course":[60,79],"profiles.":[63],"RESULTS:":[64],"We":[65],"introduce":[66],"tool,":[68],"TimeXNet,":[69],"which":[70],"identifies":[71],"sub-networks":[74,143,237],"temporal":[76],"paths":[77,111,175],"using":[78],"context":[85],"weighted":[88],"regulatory":[90],"protein-protein":[92],"network.":[94,213],"TimeXNet":[95,124,161,194,215,250,270,277],"uses":[96],"specialized":[98],"form":[99],"network":[102],"flow":[103],"optimization":[104],"approach":[105],"identify":[107],"most":[109],"probable":[110],"connecting":[112],"genes":[114],"significant":[116],"at":[120],"consecutive":[121,189],"intervals.":[123],"has":[125],"been":[126],"extensively":[127],"evaluated":[128],"for":[129,281],"its":[130],"ability":[131],"novel":[134,167],"regulators":[135,168],"their":[137],"associated":[138],"within":[140,176,191],"mouse":[146],"innate":[147],"immune":[148],"yeast":[152],"osmotic":[153],"stress":[154],"response.":[155],"Compared":[156],"other":[158,247],"similar":[159,248],"methods,":[160],"identified":[162],"up":[163],"50%":[165],"more":[166],"independent":[170],"experimental":[171],"datasets.":[172],"It":[173,242],"predicted":[174],"greater":[178],"number":[179],"known":[181],"longer":[184],"overlaps":[185],"(up":[186],"7":[188],"edges)":[190],"these":[192],"pathways.":[193],"was":[195],"also":[196],"shown":[197],"be":[199,222,272],"robust":[200],"presence":[203],"varying":[205],"amounts":[206],"noise":[208],"CONCLUSIONS:":[214],"is":[216,243,251,278],"reliable":[218],"tool":[219],"that":[220],"study":[225],"stimuli":[229],"through":[230],"identification":[232],"time-dependent":[234],"diverse":[239],"biological":[240],"systems.":[241],"significantly":[244],"better":[245],"than":[246],"tools.":[249],"implemented":[252],"Java":[254],"as":[255],"stand-alone":[257],"application":[258],"supported":[260],"on":[261],"Linux,":[262],"MS":[263],"Windows":[264],"Macintosh.":[266],"The":[267],"output":[268],"directly":[273],"viewed":[274],"Cytoscape.":[276],"freely":[279],"non-commercial":[282],"users.":[283]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}