title: Extracting regulatory networks of Escherichia coli from RegulonDB.
abstract: RegulonDB contains the largest and currently best-known data set on transcriptional regulation in a single free-living organism, that of Escherichia coli K-12 (Gama-Castro et al. Nucleic Acids Res 36:D120-D124, 2008). This organized knowledge has been the gold standard for the implementation of bioinformatic predictive methods on gene regulation in bacteria (Collado-Vides et al. J Bacteriol 191:23-31, 2009). Given the complexity of different types of interactions, the difficulty of visualizing in a single figure of the whole network, and the different uses of this knowledge, we are making available different views of the genetic network. This chapter describes case studies about how to access these views, via precomputed files, web services and SQL, including sigma-gene relationships corresponding to transcription of alternative RNA polymerase holoenzyme promoters; as well as, transcription factor (TF)-genes, TF-operons, TF-TF, and TF-regulon interactions. 17.
authors.affiliation: Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: Irma
authors.initials: I
authors.lastname: Martínez-Flores
authors.forename: Alejandra
authors.initials: A
authors.lastname: López-Fuentes
authors.forename: Jair Santiago
authors.initials: JS
authors.lastname: García-Sotelo
authors.forename: Liliana
authors.initials: L
authors.lastname: Porrón-Sotelo
authors.forename: Hilda
authors.initials: H
authors.lastname: Solano
authors.forename: Luis
authors.initials: L
authors.lastname: Muñiz-Rascado
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D020407:Internet; D009876:Operon / Q000235:genetics; D018085:Regulon / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors