{"id":"https://openalex.org/W2138973161","doi":"https://doi.org/10.1093/bioinformatics/btg347","title":"Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data","display_name":"Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data","publication_year":2003,"publication_date":"2003-10-10","ids":{"openalex":"https://openalex.org/W2138973161","doi":"https://doi.org/10.1093/bioinformatics/btg347","mag":"2138973161","pmid":"https://pubmed.ncbi.nlm.nih.gov/14555624"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg347","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg347","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1917/48904456/bioinformatics_19_15_1917.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1917/48904456/bioinformatics_19_15_1917.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100610506","display_name":"Jiang Qian","orcid":"https://orcid.org/0000-0002-0476-3596"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I2802697821","display_name":"Johns Hopkins Bayview Medical Center","ror":"https://ror.org/04pwc8466","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436","https://openalex.org/I2802697821"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jiang Qian","raw_affiliation_strings":["Department of Ophthalmology, Johns Hopkins Medical School, Baltimore, MD 21287, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ophthalmology, Johns Hopkins Medical School, Baltimore, MD 21287, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436","https://openalex.org/I2802697821"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112213111","display_name":"Jimmy Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jimmy Lin","raw_affiliation_strings":["Johns Hopkins University ("],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins University (","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020382415","display_name":"Nicholas M. Luscombe","orcid":"https://orcid.org/0000-0001-5293-4778"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas M. Luscombe","raw_affiliation_strings":["Yale University  ;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yale University  ;","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067174340","display_name":"Haiyuan Yu","orcid":"https://orcid.org/0000-0001-7597-6049"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haiyuan Yu","raw_affiliation_strings":["Yale University  ;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yale University  ;","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Yale University  ;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yale University  ;","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100610506"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436","https://openalex.org/I2802697821"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.1185,"has_fulltext":false,"cited_by_count":125,"citation_normalized_percentile":{"value":0.95033198,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"15","first_page":"1917","last_page":"1926"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8057000041007996,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8057000041007996,"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":0.11959999799728394,"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":0.04230000078678131,"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/computational-biology","display_name":"Computational biology","score":0.6941475868225098},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6124483942985535},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.6047550439834595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5379076600074768},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5282952785491943},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.49265962839126587},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4815424084663391},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.4796733856201172},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47754204273223877},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4476465880870819},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4272104799747467},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.416316419839859},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41288265585899353},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3315581679344177},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24555310606956482}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6941475868225098},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6124483942985535},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6047550439834595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5379076600074768},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5282952785491943},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.49265962839126587},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4815424084663391},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.4796733856201172},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47754204273223877},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4476465880870819},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4272104799747467},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.416316419839859},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41288265585899353},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3315581679344177},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24555310606956482}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018390","descriptor_name":"Gene Targeting","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018390","descriptor_name":"Gene Targeting","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018390","descriptor_name":"Gene Targeting","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},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btg347","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg347","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1917/48904456/bioinformatics_19_15_1917.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"},{"id":"pmid:14555624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14555624","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:eprints.ucl.ac.uk.OAI2:1344600","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1344600/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BIOINFORMATICS , 19 (15) pp. 1917-1926. (2003)","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg347","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg347","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1917/48904456/bioinformatics_19_15_1917.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1516042217","https://openalex.org/W1536240214","https://openalex.org/W1553589824","https://openalex.org/W1941659294","https://openalex.org/W1950892569","https://openalex.org/W1966645907","https://openalex.org/W1969630923","https://openalex.org/W1994352206","https://openalex.org/W2006398572","https://openalex.org/W2017200304","https://openalex.org/W2026882865","https://openalex.org/W2065996794","https://openalex.org/W2099189600","https://openalex.org/W2102794349","https://openalex.org/W2103453943","https://openalex.org/W2112221859","https://openalex.org/W2118628540","https://openalex.org/W2121298930","https://openalex.org/W2126602684","https://openalex.org/W2137683543","https://openalex.org/W2139162927","https://openalex.org/W2139212933","https://openalex.org/W2140115103","https://openalex.org/W2148603752","https://openalex.org/W2149684865","https://openalex.org/W2150926065","https://openalex.org/W2154391529","https://openalex.org/W2154514071","https://openalex.org/W2156909104","https://openalex.org/W2161477969","https://openalex.org/W2161646573"],"related_works":["https://openalex.org/W1557094818","https://openalex.org/W2183246718","https://openalex.org/W2099261052","https://openalex.org/W3209204065","https://openalex.org/W2105707930","https://openalex.org/W1755711892","https://openalex.org/W2160907113","https://openalex.org/W2090763504","https://openalex.org/W2070813941","https://openalex.org/W3046510185"],"abstract_inverted_index":{"MOTIVATION:":[0],"Defining":[1],"regulatory":[2,108,192],"networks,":[3],"linking":[4],"transcription":[5,42,90,112,246],"factors":[6,113],"(TFs)":[7],"to":[8,84,105,141,220,240],"their":[9,97],"targets,":[10],"is":[11,47,168,218,263],"a":[12,41,89,137,143,235,244],"central":[13],"problem":[14],"in":[15,69,114],"post-genomic":[16],"biology.":[17],"One":[18],"might":[19],"imagine":[20],"one":[21],"could":[22],"readily":[23],"determine":[24],"these":[25,216],"networks":[26],"through":[27,183],"inspection":[28],"of":[29,40,88,146,163,177,190,260],"gene":[30],"expression":[31,38,98,123],"data.":[32],"However,":[33],"the":[34,37,54,86,107,115,121,164,188,199,210,221,226,254,261,266],"relationship":[35],"between":[36,96,212,225],"timecourse":[39],"factor":[43,91,247],"and":[44,56,132,149,215],"its":[45],"target":[46],"not":[48,65],"obvious":[49],"(e.g.":[50],"simple":[51],"correlation":[52],"over":[53],"timecourse),":[55],"current":[57],"analysis":[58],"methods,":[59],"such":[60],"as":[61],"hierarchical":[62],"clustering,":[63],"have":[64],"been":[66],"very":[67],"successful":[68],"deciphering":[70],"them.":[71],"RESULTS:":[72],"Here":[73],"we":[74,102,173,208],"introduce":[75],"an":[76],"approach":[77],"based":[78,119],"on":[79,120,136,265],"support":[80],"vector":[81],"machines":[82],"(SVMs)":[83],"predict":[85,106],"targets":[87,109,249],"by":[92,195],"identifying":[93],"subtle":[94],"relationships":[95,180,262],"profiles.":[99],"In":[100],"particular,":[101],"used":[103],"SVMs":[104],"for":[110,170],"36":[111],"Saccharomyces":[116],"cerevisiae":[117],"genome":[118],"microarray":[122],"data":[124,138,154],"from":[125,201],"many":[126],"different":[127],"physiological":[128],"conditions.":[129],"We":[130,185,229],"trained":[131],"tested":[133],"our":[134,178,191,213],"SVM":[135],"set":[139],"constructed":[140],"include":[142],"significant":[144],"number":[145],"both":[147],"positive":[148],"negative":[150],"examples,":[151],"directly":[152],"addressing":[153],"imbalance":[155],"issues.":[156],"This":[157],"was":[158],"non-trivial":[159],"given":[160,245],"that":[161,175,231],"most":[162],"known":[165],"experimental":[166],"information":[167],"only":[169],"positives.":[171],"Overall,":[172,207],"found":[174],"63%":[176],"TF-target":[179],"were":[181],"confirmed":[182],"cross-validation.":[184],"further":[186],"assessed":[187],"performance":[189],"network":[193,233,259],"identifications":[194],"comparing":[196],"them":[197],"with":[198,238,243],"results":[200,214],"two":[202,227],"recent":[203],"genome-wide":[204],"ChIP-chip":[205],"experiments.":[206,228],"find":[209,230],"agreement":[211,222],"experiments":[217],"comparable":[219],"(albeit":[223],"low)":[224],"this":[232],"has":[234],"delocalized":[236],"structure":[237],"respect":[239],"chromosomal":[241],"positioning,":[242],"having":[248],"spread":[250],"fairly":[251],"uniformly":[252],"across":[253],"genome.":[255],"AVAILABILITY:":[256],"The":[257],"overall":[258],"available":[264],"web":[267],"at":[268],"http://bioinfo.mbb.yale.edu/expression/echipchip":[269]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":6}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
