title: The comprehensive updated regulatory network of Escherichia coli K-12.
abstract: BACKGROUND
  Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. coli transcription initiation and operons, providing in both the RegulonDB and EcoCyc databases the largest electronically encoded network available. A paper published recently by Ma et al. (2004) showed several differences in the versions of the network present in these two databases. Discrepancies have been corrected, annotations from this and other groups (Shen-Orr et al., 2002) have been added, making the RegulonDB and EcoCyc databases the largest comprehensive and constantly curated regulatory network of E. coli K-12.
  
  
  RESULTS
  Several groups have been using these curated data as part of their bioinformatics and systems biology projects, in combination with external data obtained from other sources, thus enlarging the dataset initially obtained from either RegulonDB or EcoCyc of the E. coli K12 regulatory network. We kindly obtained from the groups of Uri Alon and Hong-Wu Ma the interactions they have added to enrich their public versions of the E. coli regulatory network. These were used to search for original references and curate them with the same standards we use regularly, adding in several cases the original references (instead of reviews or missing references), as well as adding the corresponding experimental evidence codes. We also corrected all discrepancies in the two databases available as explained below.
  
  
  CONCLUSIONS
  One hundred and fifty new interactions have been added to our databases as a result of this specific curation effort, in addition to those added as a result of our continuous curation work. RegulonDB gene names are now based on those of EcoCyc to avoid confusion due to gene names and synonyms, and the public releases of RegulonDB and EcoCyc are henceforth synchronized to avoid confusion due to different versions. Public flat files are available providing direct access to the regulatory network interactions thus avoiding errors due to differences in database modelling and representation. The regulatory network available in RegulonDB and EcoCyc is the most comprehensive and regularly updated electronically-encoded regulatory network of E. coli K-12.
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave EK207, Menlo Park CA 94025 USA. heladia@ccg.unam.mx
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos-Zavaleta
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: Martín
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Mónica I
authors.initials: MI
authors.lastname: Peñaloza-Spínola
authors.forename: Agustino
authors.initials: A
authors.lastname: Martínez-Antonio
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D048168:Escherichia coli K12 / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D029968:Escherichia coli Proteins