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.
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Daniela
authors.initials: D
authors.lastname: Ledezma-Tejeida
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Luis
authors.initials: L
authors.lastname: Muñiz-Rascado
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Jair Santiago
authors.initials: JS
authors.lastname: García-Sotelo
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Kevin
authors.initials: K
authors.lastname: Alquicira-Hernández
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Irma
authors.initials: I
authors.lastname: Martínez-Flores
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Lucia
authors.initials: L
authors.lastname: Pannier
authors.affiliation: UMR_S 1090 TAGC, INSERM, Marseille, 13000 France.
authors.forename: Jaime Abraham
authors.initials: JA
authors.lastname: Castro-Mondragón
authors.affiliation: Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Juriquilla 76230, Santiago de Querétaro, QRO, Mexico.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Medina-Rivera
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Hilda
authors.initials: H
authors.lastname: Solano-Lira
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: César
authors.initials: C
authors.lastname: Bonavides-Martínez
authors.affiliation: Departamento de Microbiologia Molecular, IBT, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Pérez-Rueda
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Shirley
authors.initials: S
authors.lastname: Alquicira-Hernández
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Liliana
authors.initials: L
authors.lastname: Porrón-Sotelo
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Alejandra
authors.initials: A
authors.lastname: López-Fuentes
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Hernández-Koutoucheva
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico.
authors.forename: Víctor
authors.initials: V
authors.lastname: Del Moral-Chávez
authors.affiliation: Institute of Computational Linguistics, University of Zurich, Binzmühlestrasse 14, CH-8050 Zurich, Switzerland.
authors.forename: Fabio
authors.initials: F
authors.lastname: Rinaldi
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico collado@ccg.unam.mx.
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D016000:Cluster Analysis; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D009876:Operon; D056510:Position-Specific Scoring Matrices; D058727:RNA, Small Untranslated / Q000378:metabolism; D018085:Regulon; D014157:Transcription Factors / Q000145:classification
chemical_list: D058727:RNA, Small Untranslated; D014157:Transcription Factors