{"id":"https://openalex.org/W2000567731","doi":"https://doi.org/10.1101/gr.2439804","title":"Elucidation of Gene Interaction Networks Through Time-Lagged Correlation Analysis of Transcriptional Data","display_name":"Elucidation of Gene Interaction Networks Through Time-Lagged Correlation Analysis of Transcriptional Data","publication_year":2004,"publication_date":"2004-08-01","ids":{"openalex":"https://openalex.org/W2000567731","doi":"https://doi.org/10.1101/gr.2439804","mag":"2000567731","pmid":"https://pubmed.ncbi.nlm.nih.gov/15289483","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/509275"},"language":"en","primary_location":{"id":"doi:10.1101/gr.2439804","doi":"https://doi.org/10.1101/gr.2439804","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.2439804","pdf_url":"http://genome.cshlp.org/content/14/8/1654.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"http://genome.cshlp.org/content/14/8/1654.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109866423","display_name":"William A. Schmitt","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William A. Schmitt","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002484489","display_name":"R. Michael Raab","orcid":"https://orcid.org/0000-0001-9955-8538","observed_orcids":["https://orcid.org/0000-0001-9955-8538"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Michael Raab","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009763658","display_name":"Gregory N Stephanopoulos","orcid":"https://orcid.org/0000-0001-6909-4568","observed_orcids":["https://orcid.org/0000-0001-6909-4568"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gregory Stephanopoulos","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":98,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"8","first_page":"1654","last_page":"1663"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7231000065803528,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7231000065803528,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2070000022649765,"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/T10342","display_name":"Circadian rhythm and melatonin","score":0.008299999870359898,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-interaction-networks","display_name":"gene interaction networks","score":0.8320000171661377},{"id":"https://openalex.org/keywords/synechocystis-sp-pcc-6803","display_name":"Synechocystis sp. PCC 6803","score":0.9610000252723694},{"id":"https://openalex.org/keywords/cyanobacteria","display_name":"cyanobacteria","score":0.7440000176429749},{"id":"https://openalex.org/keywords/light-intensity-response","display_name":"light intensity response","score":0.6830000281333923},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.7879999876022339},{"id":"https://openalex.org/keywords/photosynthesis","display_name":"photosynthesis","score":0.4880000054836273},{"id":"https://openalex.org/keywords/photosystem-i","display_name":"photosystem I","score":0.8600000143051147},{"id":"https://openalex.org/keywords/photosystem-ii","display_name":"photosystem II","score":1.0},{"id":"https://openalex.org/keywords/co2-fixation","display_name":"CO2 fixation","score":0.9409999847412109},{"id":"https://openalex.org/keywords/gene-co-expression","display_name":"gene co-expression","score":0.4480000138282776},{"id":"https://openalex.org/keywords/temporal-gene-expression","display_name":"temporal gene expression","score":0.6460000276565552}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8247242569923401},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6834580302238464},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.6056692004203796},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5854250192642212},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5636172294616699},{"id":"https://openalex.org/C3020368824","wikidata":"https://www.wikidata.org/wiki/Q6546192","display_name":"Light intensity","level":2,"score":0.529283344745636},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.45769932866096497},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3913782238960266},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.25305676460266113},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008027","descriptor_name":"Light","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1101/gr.2439804","doi":"https://doi.org/10.1101/gr.2439804","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.2439804","pdf_url":"http://genome.cshlp.org/content/14/8/1654.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:509275","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/509275","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,"listed_in":[],"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":"Genome Res","raw_type":"Text"},{"id":"pmid:15289483","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15289483","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,"listed_in":[],"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":"Genome research","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1101/gr.2439804","doi":"https://doi.org/10.1101/gr.2439804","is_oa":true,"landing_page_url":"https://doi.org/10.1101/gr.2439804","pdf_url":"http://genome.cshlp.org/content/14/8/1654.full.pdf","source":{"id":"https://openalex.org/S43092948","display_name":"Genome Research","issn_l":"1088-9051","issn":["1088-9051","1549-5469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315909","host_organization_name":"Cold Spring Harbor Laboratory Press","host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Research","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2763221673","display_name":null,"funder_award_id":"1-R01-DK58533-01","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G5329720183","display_name":"LINKING GENOMICS TO FUNCTION VIA METABOLIC PHENOTYPING","funder_award_id":"R01DK058533","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2000567731.pdf","grobid_xml":"https://content.openalex.org/works/W2000567731.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W99210128","https://openalex.org/W1571301392","https://openalex.org/W1604154267","https://openalex.org/W1969442032","https://openalex.org/W1976208596","https://openalex.org/W2020841917","https://openalex.org/W2067478206","https://openalex.org/W2077024091","https://openalex.org/W2080147211","https://openalex.org/W2083691092","https://openalex.org/W2086345724","https://openalex.org/W2089142451","https://openalex.org/W2103453943","https://openalex.org/W2104257336","https://openalex.org/W2107866839","https://openalex.org/W2109970232","https://openalex.org/W2113387206","https://openalex.org/W2120263847","https://openalex.org/W2135187880","https://openalex.org/W2135938395","https://openalex.org/W2135951244","https://openalex.org/W2148541040","https://openalex.org/W2150926065","https://openalex.org/W2162491638","https://openalex.org/W2164249947","https://openalex.org/W2611370172","https://openalex.org/W4295127969","https://openalex.org/W7099880618"],"related_works":["https://openalex.org/W108405581","https://openalex.org/W7096082536","https://openalex.org/W2533924017","https://openalex.org/W2562871619","https://openalex.org/W4245477987","https://openalex.org/W2140938953","https://openalex.org/W53766694","https://openalex.org/W7095275900","https://openalex.org/W140796358","https://openalex.org/W2152858250"],"abstract_inverted_index":{"The":[0,61,160],"photosynthetic":[1],"cyanobacterium":[2],"Synechocystis":[3,33,182],"sp.":[4,34,183],"strain":[5],"PCC":[6],"6803":[7],"uses":[8],"a":[9,140],"complex":[10],"genetic":[11,71],"program":[12,26],"to":[13,18,35,49],"control":[14],"its":[15],"physiological":[16],"response":[17],"alternating":[19],"light":[20,39,100,123],"conditions.":[21],"To":[22],"study":[23],"this":[24,127,199],"regulatory":[25],"time-series":[27],"experiments":[28],"were":[29,47],"conducted":[30],"by":[31,74,129],"exposing":[32],"serial":[36],"perturbations":[37],"in":[38,53,198],"intensity.":[40,124],"In":[41],"each":[42,135],"experiment":[43],"whole-genome":[44],"DNA":[45],"microarrays":[46],"used":[48],"monitor":[50],"gene":[51,173,178],"transcription":[52,79],"20-min":[54],"intervals":[55],"over":[56],"8-":[57],"and":[58,142,186,188],"16-h":[59],"periods.":[60],"data":[62],"was":[63],"analyzed":[64],"using":[65,130],"time-lagged":[66,114,148],"correlation":[67],"analysis,":[68],"which":[69],"identifies":[70],"interaction":[72],"networks":[73,88],"constructing":[75],"correlations":[76],"between":[77],"time-shifted":[78],"profiles":[80,115,149],"with":[81,121,155],"different":[82,165],"levels":[83],"of":[84,91,111,137,171],"statistical":[85],"confidence.":[86],"These":[87],"allow":[89],"inference":[90],"putative":[92],"cause-effect":[93],"relationships":[94],"among":[95],"the":[96,122,131,156],"organism's":[97],"genes.":[98,169],"Using":[99],"intensity":[101],"as":[102,139,181],"our":[103],"initial":[104],"input":[105],"signal,":[106],"we":[107],"identified":[108],"six":[109],"groups":[110,166,174],"genes":[112,138,146],"whose":[113,147],"possessed":[116,150],"significant":[117,151],"correlation,":[118,152],"or":[119,153],"anti-correlation,":[120,154],"We":[125],"expanded":[126],"network":[128,162],"average":[132,158],"profile":[133],"from":[134],"group":[136],"seed,":[141],"searching":[143],"for":[144],"other":[145],"group's":[157],"profile.":[159],"final":[161],"comprised":[163],"50":[164],"containing":[167],"259":[168],"Several":[170],"these":[172],"possess":[175],"known":[176],"light-stimulated":[177],"clusters,":[179],"such":[180],"photosystems":[184],"I":[185],"II":[187],"carbon":[189],"dioxide":[190],"fixation":[191],"pathways,":[192],"while":[193],"others":[194],"represent":[195],"novel":[196],"findings":[197],"work.":[200]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":7}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}