{"id":"https://openalex.org/W2137573464","doi":"https://doi.org/10.1093/bioinformatics/btm457","title":"Context-dependent clustering for dynamic cellular state modeling of microarray gene expression","display_name":"Context-dependent clustering for dynamic cellular state modeling of microarray gene expression","publication_year":2007,"publication_date":"2007-09-10","ids":{"openalex":"https://openalex.org/W2137573464","doi":"https://doi.org/10.1093/bioinformatics/btm457","mag":"2137573464","pmid":"https://pubmed.ncbi.nlm.nih.gov/17846037"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm457","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm457","pdf_url":null,"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","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103792794","display_name":"Shinsheng Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210141710","display_name":"Institute of Statistical Science, Academia Sinica","ror":"https://ror.org/044gv5910","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210141710","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Shinsheng Yuan","raw_affiliation_strings":["1 Institute of Statistical Science, Acadmia Sinica, 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan, ROC and 2Department of Statistics, UCLA, 8125 Math Sciences Bldg. Box 951554 Los Angeles, CA 90095-1554, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute of Statistical Science, Acadmia Sinica, 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan, ROC and 2Department of Statistics, UCLA, 8125 Math Sciences Bldg. Box 951554 Los Angeles, CA 90095-1554, USA","institution_ids":["https://openalex.org/I4210141710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025824844","display_name":"Ker-Chau Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210141710","display_name":"Institute of Statistical Science, Academia Sinica","ror":"https://ror.org/044gv5910","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210141710","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Ker-Chau Li","raw_affiliation_strings":["1 Institute of Statistical Science, Acadmia Sinica, 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan, ROC and 2Department of Statistics, UCLA, 8125 Math Sciences Bldg. Box 951554 Los Angeles, CA 90095-1554, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute of Statistical Science, Acadmia Sinica, 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan, ROC and 2Department of Statistics, UCLA, 8125 Math Sciences Bldg. Box 951554 Los Angeles, CA 90095-1554, USA","institution_ids":["https://openalex.org/I4210141710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025824844"],"corresponding_institution_ids":["https://openalex.org/I4210141710"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6662,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.69096725,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"22","first_page":"3039","last_page":"3047"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2101999968290329,"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":0.2101999968290329,"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":0.18719999492168427,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.11150000244379044,"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/context","display_name":"Context (archaeology)","score":0.6811986565589905},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6247975826263428},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5656849145889282},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5405430197715759},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.5144708156585693},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.5109452605247498},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4644947350025177},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4570254981517792},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4480552673339844},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.44741761684417725},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.44684308767318726},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4370340406894684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36686038970947266},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.334603875875473},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31774061918258667},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16347166895866394},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.11330032348632812},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08489617705345154}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6811986565589905},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6247975826263428},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5656849145889282},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5405430197715759},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.5144708156585693},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5109452605247498},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4644947350025177},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4570254981517792},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4480552673339844},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.44741761684417725},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.44684308767318726},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4370340406894684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36686038970947266},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.334603875875473},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31774061918258667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16347166895866394},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.11330032348632812},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08489617705345154},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm457","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm457","pdf_url":null,"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"},{"id":"pmid:17846037","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17846037","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1533936090","https://openalex.org/W1981778933","https://openalex.org/W1983923347","https://openalex.org/W1989076816","https://openalex.org/W2011768728","https://openalex.org/W2018843280","https://openalex.org/W2024532878","https://openalex.org/W2049633694","https://openalex.org/W2069645361","https://openalex.org/W2080498142","https://openalex.org/W2087684630","https://openalex.org/W2098994369","https://openalex.org/W2102794349","https://openalex.org/W2103453943","https://openalex.org/W2103697116","https://openalex.org/W2103835486","https://openalex.org/W2105860794","https://openalex.org/W2109363337","https://openalex.org/W2126602684","https://openalex.org/W2135187880","https://openalex.org/W2139845570","https://openalex.org/W2142305821","https://openalex.org/W2142433578","https://openalex.org/W2142610549","https://openalex.org/W2146264532","https://openalex.org/W2146646206","https://openalex.org/W2148541040","https://openalex.org/W2150473224","https://openalex.org/W2150926065","https://openalex.org/W2160875291","https://openalex.org/W2262161731"],"related_works":["https://openalex.org/W1996185163","https://openalex.org/W170658859","https://openalex.org/W2081127504","https://openalex.org/W1483316219","https://openalex.org/W4310366902","https://openalex.org/W3023720143","https://openalex.org/W2183420549","https://openalex.org/W2490137852","https://openalex.org/W2107563406","https://openalex.org/W2039699813"],"abstract_inverted_index":{"MOTIVATION:":[0],"High-throughput":[1],"expression":[2,14,45,139,169,178,190,200],"profiling":[3],"allows":[4],"researchers":[5],"to":[6,18,101,117,126,211,266],"study":[7,130],"gene":[8,84,138],"activities":[9],"globally.":[10],"Genes":[11],"with":[12,198],"similar":[13],"profiles":[15,179],"are":[16,47,256],"likely":[17],"encode":[19],"proteins":[20],"that":[21,228],"may":[22],"participate":[23],"in":[24,42,71,103,258],"a":[25,79,112,263],"common":[26,57],"structural":[27],"complex,":[28],"metabolic":[29],"pathway":[30,240],"or":[31,98],"biological":[32,270],"process.":[33],"Many":[34],"clustering,":[35],"classification":[36],"and":[37,150,176,220,249],"dimension":[38],"reduction":[39],"approaches,":[40],"powerful":[41],"elucidating":[43],"the":[44,53,89,119,127,135,143,157,168,189,199,208,212,217,231,268],"data,":[46],"based":[48],"on":[49],"this":[50,56,75],"rationale.":[51],"However,":[52],"converse":[54],"of":[55,161,170,191,201,206,214],"perception":[58],"can":[59,95,180],"be":[60,96,181],"misleading.":[61],"In":[62,74],"fact,":[63],"many":[64,185],"biologically":[65],"related":[66,93],"genes":[67,94,153,245],"turn":[68],"out":[69],"uncorrelated":[70],"expression.":[72],"RESULTS:":[73],"article,":[76],"we":[77,223],"present":[78],"novel":[80],"method":[81,116,261],"for":[82,131,225,236],"investigating":[83],"co-expression":[85,144],"patterns.":[86],"We":[87,110,123,141],"assume":[88],"correlation":[90,173,215],"between":[91,146,174,216],"functionally":[92],"strengthened":[97],"weakened":[99],"according":[100],"changes":[102],"some":[104],"relevant,":[105],"yet":[106],"unknown,":[107],"cellular":[108,120,226],"states.":[109],"develop":[111],"context-dependent":[113],"clustering":[114],"(CDC)":[115],"model":[118],"state":[121],"variable.":[122],"apply":[124],"it":[125],"transcription":[128,147,192],"regulatory":[129],"Saccharomyces":[132],"cerevisiae,":[133],"using":[134],"Stanford":[136],"cell-cycle":[137],"data.":[140,274],"investigate":[142],"patterns":[145],"factors":[148,193],"(TFs)":[149],"their":[151,202],"target":[152,203],"(TGs)":[154],"predicted":[155],"by":[156,242,247,254],"genome-wide":[158],"location":[159],"analysis":[160],"Harbison":[162],"et":[163],"al.":[164],"Since":[165],"TF":[166,221],"regulates":[167],"its":[171],"TGs,":[172],"TFs":[175],"TGs":[177],"expected.":[182],"But":[183],"as":[184],"authors":[186],"have":[187],"observed,":[188],"do":[194],"not":[195],"correlate":[196],"well":[197],"genes.":[204],"Instead":[205],"attributing":[207],"main":[209],"reason":[210],"lack":[213],"transcript":[218],"abundance":[219],"activity,":[222],"search":[224],"conditions":[227],"would":[229],"facilitate":[230],"TF-TG":[232],"correlation.":[233],"The":[234],"results":[235],"sulfur":[237],"amino":[238],"acid":[239],"regulation":[241,246,253],"MET4,":[243],"respiratory":[244],"HAP4,":[248],"mitotic":[250],"cell":[251],"cycle":[252],"ACE2/SWI5":[255],"discussed":[257],"detail.":[259],"Our":[260],"suggests":[262],"new":[264],"way":[265],"understand":[267],"complex":[269],"system":[271],"from":[272],"microarray":[273]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}