RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

Authors:
  • SGSocorro Gama-Castro
    Socorro Gama-Castro
  • EDEdgar Díaz-Peredo
    Edgar Díaz-Peredo
  • FSFabiola Sánchez-Solano
    Fabiola Sánchez-Solano
  • MPMartín Peralta-Gil
    Martín Peralta-Gil
  • DGDelfino Garcia-Alonso
    Delfino Garcia-Alonso
  • VJVerónica Jiménez-Jacinto
    Verónica Jiménez-Jacinto
  • ASAlberto Santos-Zavaleta
    Alberto Santos-Zavaleta
  • CBCésar Bonavides-Martínez
    César Bonavides-Martínez
  • JCJulio Collado-Vides
    Julio Collado-Vides
Publisher website
Google Scholar
Abstract
RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their sigma type, binding sites of specific transcriptional regulators (TRs), their organization into 'regulatory phrases', active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs. The current version has been expanded to include information beyond specific mechanisms aimed at gathering different growth conditions and the associated induced and/or repressed genes. RegulonDB is now linked with Swiss-Prot, with microarray databases, and with a suite of programs to analyze and visualize microarray experiments. We provide a summary of the biological knowledge contained in RegulonDB and describe the major changes in the design of the database. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/.

This publication has 20 references indexed in Scilit: