{"doi":"10.1093/nar/gkv1156","title":"RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond","abstract":null,"journal":"Nucleic Acids Research","year":2016,"id":599429,"datarank":0.9464877417339775,"base_score":6.309918278226516,"endowment":6.309918278226516,"self_citation_contribution":0.9464877417339775,"citation_network_contribution":0.0,"self_endowment_contribution":0.9464877417339775,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":549,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":527495,"name":"Heladia Salgado","orcid":"0000-0002-3166-5801","position":1,"is_corresponding":false},{"id":621629,"name":"Alberto Santos-Zavaleta","orcid":"0000-0002-2178-4006","position":2,"is_corresponding":false},{"id":955097,"name":"Daniela Ledezma-Tejeida","orcid":"0000-0002-2055-417X","position":3,"is_corresponding":false},{"id":621627,"name":"Luis Muñiz-Rascado","orcid":"0000-0003-2941-2482","position":4,"is_corresponding":false},{"id":848082,"name":"Jair Santiago García-Sotelo","orcid":"0000-0002-9462-2737","position":5,"is_corresponding":false},{"id":1536244,"name":"Kevin Alquicira-Hernández","orcid":null,"position":6,"is_corresponding":false},{"id":1536245,"name":"Irma Martínez-Flores","orcid":null,"position":7,"is_corresponding":false},{"id":1536246,"name":"Lucia Pannier","orcid":null,"position":8,"is_corresponding":false},{"id":1536247,"name":"Jaime Abraham Castro-Mondragón","orcid":null,"position":9,"is_corresponding":false},{"id":118504,"name":"Alejandra Medina-Rivera","orcid":null,"position":10,"is_corresponding":false},{"id":581861,"name":"Hilda Solano-Lira","orcid":null,"position":11,"is_corresponding":false},{"id":621625,"name":"César Bonavides-Martínez","orcid":"0000-0003-4966-138X","position":12,"is_corresponding":false},{"id":1536248,"name":"Ernesto Pérez-Rueda","orcid":null,"position":13,"is_corresponding":false},{"id":848081,"name":"Shirley Alquicira-Hernández","orcid":"0000-0002-4709-2008","position":14,"is_corresponding":false},{"id":1536249,"name":"Liliana Porrón-Sotelo","orcid":null,"position":15,"is_corresponding":false},{"id":1536250,"name":"Alejandra López-Fuentes","orcid":null,"position":16,"is_corresponding":false},{"id":1016814,"name":"Anastasia Hernández-Koutoucheva","orcid":"0000-0002-0197-9092","position":17,"is_corresponding":false},{"id":1536251,"name":"Víctor Del Moral-Chávez","orcid":null,"position":18,"is_corresponding":false},{"id":581172,"name":"Fabio Rinaldi","orcid":"0000-0001-5718-5462","position":19,"is_corresponding":false},{"id":12903,"name":"Julio Collado-Vides","orcid":null,"position":20,"is_corresponding":false},{"id":1536243,"name":"Socorro Gama-Castro","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond","abstract":"RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates the scattered scientific knowledge of the best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts of data. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Here, we summarize our progress with RegulonDB since our last Nucleic Acids Research publication describing RegulonDB, in 2013. In addition to maintaining curation up-to-date, we report a collection of 232 interactions with small RNAs affecting 192 genes, and the complete repertoire of 189 Elementary Genetic Sensory-Response units (GENSOR units), integrating the signal, regulatory interactions, and metabolic pathways they govern. These additions represent major progress to a higher level of understanding of regulated processes. We have updated the computationally predicted transcription factors, which total 304 (184 with experimental evidence and 120 from computational predictions); we updated our position-weight matrices and have included tools for clustering them in evolutionary families. We describe our semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for 'neighborhood' genes to known operons and regulons, and computational developments.","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"26527724","pmcid":"PMC4702833","openalex_id":null,"authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R01GM110597","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"2U24GM077678-24A1","title":"The EcoCyc Model Organism Database for Escherichia coli [SRI Proposal ECU 14-631]"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM110597-03","title":"HIGH THROUGHPUT LITERATURE CURATION OF GENETIC REGULATION IN BACTERIAL MODELS"}],"total_grants":3,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/44/D1/D133/16661521/gkv1156.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/44/D1/D133/16661521/gkv1156.pdf","host_type":"publisher"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4702833","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC4702833","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC4702833?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1093/nar/gkv1156","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/26527724","host_type":""},{"url":"http://dx.doi.org/10.1093/nar/gkv1156","host_type":""},{"url":"https://amu.hal.science/hal-01460125v1","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkv1156","host_type":""},{"url":"https://sonar.ch/global/documents/287200","host_type":""}],"fields_of_study":["0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Escherichia coli K12","Transcription Factors","Cluster Analysis","Gene Expression Regulation, Bacterial","Operon","Regulon","Databases, Genetic","Gene Regulatory Networks","Position-Specific Scoring Matrices","RNA, Small Untranslated"],"keywords":["Escherichia coli K12","Gene Expression Regulation, Bacterial","Regulon","[SDV] Life Sciences [q-bio]","Databases, Genetic","Operon","Database Issue","Cluster Analysis","Position-Specific Scoring Matrices","RNA, Small Untranslated","Gene Regulatory Networks","Transcription Factors"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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