{"id":"https://openalex.org/W2152824658","doi":"https://doi.org/10.1093/nar/gkh140","title":"RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12","display_name":"RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12","publication_year":2003,"publication_date":"2003-12-18","ids":{"openalex":"https://openalex.org/W2152824658","doi":"https://doi.org/10.1093/nar/gkh140","mag":"2152824658","pmid":"https://pubmed.ncbi.nlm.nih.gov/14681419"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkh140","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh140","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D303/7622238/gkh140.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D303/7622238/gkh140.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091338305","display_name":"Heladia Salgado","orcid":"https://orcid.org/0000-0002-3166-5801"},"institutions":[{"id":"https://openalex.org/I4210116760","display_name":"Universidad Americana de Morelos","ror":"https://ror.org/02cf9zs75","country_code":"MX","type":"education","lineage":["https://openalex.org/I4210116760"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"H. Salgado","raw_affiliation_strings":["Program of Computational Genomics, CIFN, UNAM. A.P. 565-A Cuernavaca, Morelos 62100, Mexico","Program of Computational Genomics, CIFN, UNAM. A.P. 565\u2010A Cuernavaca, Morelos 62100, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program of Computational Genomics, CIFN, UNAM. A.P. 565-A Cuernavaca, Morelos 62100, Mexico","institution_ids":["https://openalex.org/I4210116760"]},{"raw_affiliation_string":"Program of Computational Genomics, CIFN, UNAM. A.P. 565\u2010A Cuernavaca, Morelos 62100, Mexico","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091338305"],"corresponding_institution_ids":["https://openalex.org/I4210116760"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":15.2791,"has_fulltext":true,"cited_by_count":262,"citation_normalized_percentile":{"value":0.99544943,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"90001","first_page":"303D","last_page":"306"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9972000122070312,"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/biology","display_name":"Biology","score":0.94428551197052},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.8642950057983398},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.8146648406982422},{"id":"https://openalex.org/keywords/escherichia-coli-proteins","display_name":"Escherichia coli Proteins","score":0.5750541687011719},{"id":"https://openalex.org/keywords/trp-operon","display_name":"trp operon","score":0.5101013779640198},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.48567473888397217},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.44684261083602905},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3009042739868164},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.16048085689544678}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.94428551197052},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.8642950057983398},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.8146648406982422},{"id":"https://openalex.org/C2908821069","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli Proteins","level":4,"score":0.5750541687011719},{"id":"https://openalex.org/C96601446","wikidata":"https://www.wikidata.org/wiki/Q287043","display_name":"trp operon","level":5,"score":0.5101013779640198},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.48567473888397217},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.44684261083602905},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3009042739868164},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.16048085689544678}],"mesh":[{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkh140","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh140","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D303/7622238/gkh140.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:14681419","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14681419","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:figshare.com:article/1283995","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/RegulonDB_version_4_0_transcriptional_regulation_operon_organization_and_growth_conditions_in_Escherichia_coli_K_12/1283995","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:308874","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/308874","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"doi:10.6084/m9.figshare.1283995.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.1283995.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/nar/gkh140","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh140","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D303/7622238/gkh140.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.550000011920929}],"awards":[{"id":"https://openalex.org/G226119940","display_name":null,"funder_award_id":"1-R01-RR07861","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G4976180702","display_name":null,"funder_award_id":"R01 RR007861","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G5707856742","display_name":null,"funder_award_id":"GM62205-02","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152824658.pdf","grobid_xml":"https://content.openalex.org/works/W2152824658.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1582298918","https://openalex.org/W1969630923","https://openalex.org/W1975924111","https://openalex.org/W1978984420","https://openalex.org/W2025853251","https://openalex.org/W2026900488","https://openalex.org/W2036729166","https://openalex.org/W2039751039","https://openalex.org/W2106913956","https://openalex.org/W2107333582","https://openalex.org/W2108345442","https://openalex.org/W2108918329","https://openalex.org/W2109621905","https://openalex.org/W2110455321","https://openalex.org/W2110699703","https://openalex.org/W2118640842","https://openalex.org/W2136913687","https://openalex.org/W2145198449","https://openalex.org/W2154199509","https://openalex.org/W2160453515","https://openalex.org/W2165392091","https://openalex.org/W2915429056"],"related_works":["https://openalex.org/W2086425371","https://openalex.org/W1993953940","https://openalex.org/W2029113436","https://openalex.org/W2013327651","https://openalex.org/W2146502111","https://openalex.org/W156264808","https://openalex.org/W2153953146","https://openalex.org/W1603488550","https://openalex.org/W2467376097","https://openalex.org/W1481226713"],"abstract_inverted_index":{"RegulonDB":[0,119,150,162],"is":[1,79,120],"the":[2,6,18,23,113,145,153,157,160,167,170],"primary":[3],"database":[4,78],"of":[5,11,22,25,53,67,86,92,132,144,159],"major":[7,154],"international":[8],"maintained":[9],"curation":[10],"original":[12],"literature":[13],"with":[14,81,123,125,129],"experimental":[15],"knowledge":[16,147],"about":[17,36],"elements":[19],"and":[20,39,47,64,73,89,112,128,136,151],"interactions":[21],"network":[24],"transcriptional":[26,55],"regulation":[27],"in":[28,149,156],"Escherichia":[29],"coli":[30],"K-12.":[31],"This":[32],"includes":[33],"mechanistic":[34],"information":[35,102],"operon":[37],"organization":[38,59],"their":[40,48,58],"decomposition":[41],"into":[42,60],"transcription":[43],"units":[44],"(TUs),":[45],"promoters":[46,88],"sigma":[49],"type,":[50],"binding":[51,75,90],"sites":[52,91],"specific":[54,104],"regulators":[56],"(TRs),":[57],"'regulatory":[61],"phrases',":[62],"active":[63],"inactive":[65],"conformations":[66],"TRs,":[68],"as":[69,71],"well":[70],"terminators":[72],"ribosome":[74],"sites.":[76],"The":[77,94],"complemented":[80],"clearly":[82],"marked":[83],"computational":[84],"predictions":[85],"TUs,":[87],"TRs.":[93],"current":[95],"version":[96],"has":[97],"been":[98],"expanded":[99],"to":[100,134],"include":[101],"beyond":[103],"mechanisms":[105],"aimed":[106],"at":[107,169],"gathering":[108],"different":[109],"growth":[110],"conditions":[111],"associated":[114],"induced":[115],"and/or":[116],"repressed":[117],"genes.":[118],"now":[121],"linked":[122],"Swiss-Prot,":[124],"microarray":[126,138],"databases,":[127],"a":[130,142],"suite":[131],"programs":[133],"analyze":[135],"visualize":[137],"experiments.":[139],"We":[140],"provide":[141],"summary":[143],"biological":[146],"contained":[148],"describe":[152],"changes":[155],"design":[158],"database.":[161],"can":[163],"be":[164],"accessed":[165],"on":[166],"web":[168],"URL:":[171],"http://www.cifn.unam.mx/Computational_Biology/regulondb/.":[172]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":5}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}