{"id":"https://openalex.org/W2079574756","doi":"https://doi.org/10.1093/bioinformatics/btm309","title":"Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process","display_name":"Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process","publication_year":2007,"publication_date":"2007-06-06","ids":{"openalex":"https://openalex.org/W2079574756","doi":"https://doi.org/10.1093/bioinformatics/btm309","mag":"2079574756"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm309","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm309","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/16/2096/16858120/btm309.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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/16/2096/16858120/btm309.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062339398","display_name":"Laura L. Elo","orcid":"https://orcid.org/0000-0001-5648-4532"},"institutions":[{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FI","FR"],"is_corresponding":true,"raw_author_name":"Laura L. Elo","raw_affiliation_strings":["1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France"],"affiliations":[{"raw_affiliation_string":"1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France","institution_ids":["https://openalex.org/I4210140120","https://openalex.org/I155660961","https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054995351","display_name":"Henna J\u00e4rvenp\u00e4\u00e4","orcid":null},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]}],"countries":["FI","FR"],"is_corresponding":false,"raw_author_name":"Henna J\u00e4rvenp\u00e4\u00e4","raw_affiliation_strings":["1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France"],"affiliations":[{"raw_affiliation_string":"1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France","institution_ids":["https://openalex.org/I4210140120","https://openalex.org/I155660961","https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083895460","display_name":"Matej Ore\u0161i\u010d","orcid":"https://orcid.org/0000-0002-2856-9165"},"institutions":[{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FI","FR"],"is_corresponding":false,"raw_author_name":"Matej Ore\u0161i\u010d","raw_affiliation_strings":["1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France"],"affiliations":[{"raw_affiliation_string":"1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France","institution_ids":["https://openalex.org/I4210140120","https://openalex.org/I155660961","https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029683473","display_name":"Riitta Lahesmaa","orcid":"https://orcid.org/0000-0002-4782-9567"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI","FR"],"is_corresponding":false,"raw_author_name":"Riitta Lahesmaa","raw_affiliation_strings":["1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France"],"affiliations":[{"raw_affiliation_string":"1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France","institution_ids":["https://openalex.org/I4210140120","https://openalex.org/I155660961","https://openalex.org/I157536573"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016681267","display_name":"Tero Aittokallio","orcid":"https://orcid.org/0000-0002-0886-9769"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]}],"countries":["FI","FR"],"is_corresponding":false,"raw_author_name":"Tero Aittokallio","raw_affiliation_strings":["1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France"],"affiliations":[{"raw_affiliation_string":"1 Department of Mathematics, FI-20014 University of Turku, 2Turku Centre for Biotechnology, PO Box 123, FI-20521 Turku, 3VTT Biotechnology, PO Box 1500, FI-02044 Espoo, Finland and 4Systems Biology Unit, Institut Pasteur, FR-75724 Paris, France","institution_ids":["https://openalex.org/I4210140120","https://openalex.org/I155660961","https://openalex.org/I157536573"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5062339398"],"corresponding_institution_ids":["https://openalex.org/I155660961","https://openalex.org/I157536573","https://openalex.org/I4210140120"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9446,"has_fulltext":true,"cited_by_count":109,"citation_normalized_percentile":{"value":0.91384513,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"16","first_page":"2096","last_page":"2103"},"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":0.9987000226974487,"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":0.9976000189781189,"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/cutoff","display_name":"Cutoff","score":0.7540265321731567},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5960754156112671},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5495685935020447},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5006780624389648},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4966593384742737},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4559288024902344},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4076279103755951},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3756125271320343},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3599000573158264},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3581482768058777},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1725335717201233},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15535706281661987},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08577167987823486}],"concepts":[{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.7540265321731567},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5960754156112671},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5495685935020447},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5006780624389648},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4966593384742737},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4559288024902344},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4076279103755951},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3756125271320343},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3599000573158264},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3581482768058777},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1725335717201233},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15535706281661987},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08577167987823486},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btm309","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm309","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/16/2096/16858120/btm309.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm309","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm309","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/16/2096/16858120/btm309.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":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.6499999761581421}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2079574756.pdf","grobid_xml":"https://content.openalex.org/works/W2079574756.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W79940681","https://openalex.org/W425633012","https://openalex.org/W1578692400","https://openalex.org/W1592356192","https://openalex.org/W1659833910","https://openalex.org/W1904478869","https://openalex.org/W1971384289","https://openalex.org/W1992452843","https://openalex.org/W2023488690","https://openalex.org/W2034784092","https://openalex.org/W2036174202","https://openalex.org/W2044525257","https://openalex.org/W2062014401","https://openalex.org/W2072184218","https://openalex.org/W2081098333","https://openalex.org/W2102043440","https://openalex.org/W2103017472","https://openalex.org/W2104808368","https://openalex.org/W2108331169","https://openalex.org/W2110112697","https://openalex.org/W2110552598","https://openalex.org/W2112090702","https://openalex.org/W2113485564","https://openalex.org/W2139807849","https://openalex.org/W2140736261","https://openalex.org/W2142720308","https://openalex.org/W2146045333","https://openalex.org/W2155205047","https://openalex.org/W2160875291","https://openalex.org/W2161409973","https://openalex.org/W2162142896","https://openalex.org/W2170989872","https://openalex.org/W2584528809","https://openalex.org/W6636762583"],"related_works":["https://openalex.org/W3092388660","https://openalex.org/W1778838665","https://openalex.org/W1986953345","https://openalex.org/W3175879137","https://openalex.org/W2328322229","https://openalex.org/W2119262383","https://openalex.org/W4320056724","https://openalex.org/W3094919452","https://openalex.org/W1982897783","https://openalex.org/W2593123794"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Coexpression":[2],"networks":[3,45,92],"have":[4,171],"recently":[5],"emerged":[6],"as":[7,30],"a":[8,25,33,62,82,87,119],"novel":[9],"holistic":[10],"approach":[11,109],"to":[12,143,149],"microarray":[13,129],"data":[14,76,205],"analysis":[15],"and":[16,77,100,162],"interpretation.":[17],"Choosing":[18],"an":[19],"appropriate":[20],"cutoff":[21,64,88],"threshold,":[22],"above":[23],"which":[24,58,139,169],"gene\u2013gene":[26],"interaction":[27],"is":[28,32],"considered":[29],"relevant,":[31],"critical":[34],"task":[35],"in":[36,189,196],"most":[37],"network-centric":[38],"applications,":[39],"especially":[40],"when":[41],"two":[42],"or":[43,65,136],"more":[44],"are":[46,59,206],"being":[47],"compared.":[48],"Results:":[49],"We":[50],"demonstrate":[51],"that":[52],"the":[53,73,116,145,160,175,197],"performance":[54],"of":[55,75,90,106,122,168,177],"traditional":[56],"approaches,":[57],"based":[60],"on":[61,72,174],"pre-defined":[63],"significance":[66],"level,":[67],"can":[68,140],"vary":[69],"drastically":[70],"depending":[71],"type":[74],"application.":[78],"Therefore,":[79],"we":[80],"introduce":[81],"systematic":[83],"procedure":[84,117],"for":[85],"estimating":[86],"threshold":[89],"coexpression":[91],"directly":[93],"from":[94,127],"their":[95,193],"topological":[96,187],"properties.":[97],"Both":[98],"synthetic":[99],"real":[101],"datasets":[102],"show":[103],"clear":[104],"benefits":[105],"our":[107],"data-driven":[108],"under":[110],"various":[111],"practical":[112],"circumstances.":[113],"In":[114],"particular,":[115],"provides":[118,156],"robust":[120],"estimate":[121],"individual":[123],"degree":[124],"distributions,":[125],"even":[126],"multiple":[128],"studies":[130],"performed":[131],"with":[132],"different":[133],"array":[134],"platforms":[135],"experimental":[137],"designs,":[138],"be":[141],"used":[142],"discriminate":[144],"corresponding":[146],"phenotypes.":[147],"Application":[148],"human":[150],"T":[151],"helper":[152],"cell":[153],"differentiation":[154,198],"process":[155],"useful":[157],"insights":[158],"into":[159],"components":[161],"interactions":[163],"controlling":[164],"this":[165],"process,":[166],"many":[167],"would":[170],"remained":[172],"unidentified":[173],"basis":[176],"expression":[178],"change":[179],"alone.":[180],"Moreover,":[181],"several":[182],"human\u2013mouse":[183],"orthologs":[184],"showed":[185],"conserved":[186],"changes":[188],"both":[190],"systems,":[191],"suggesting":[192],"potential":[194],"importance":[195],"process.":[199],"Contact:":[200],"laliel@utu.fi":[201],"Supplementary":[202,204],"information:":[203],"available":[207],"at":[208],"Bioinformatics":[209],"online.":[210]},"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":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":8}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2016-06-24T00:00:00"}