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The analysis and expansion of regulatory binding site data in a wide range of bacteria using a semi-automatic system - RegTransBase

  • Author(s): Novichkov, Pavel
  • Cipriano, Michael
  • Kazakov, Alexey
  • Ravcheev, Dmitry
  • Arkin, Adam
  • Gelfand, Mikhail
  • Dubchak, Inna
  • et al.
Abstract

RegTransBase, a database describing regulatory interactions in prokaryotes, has been developed as a component of the MicrobesOnline/RegTransBase framework successfully used for interpretation of microbial stress response and metal reduction pathways. It is manually curated and based on published scientific literature. RegTransBase describes a large number of regulatory interactions and contains experimental data which investigates regulation with known elements. It is available at http://regtransbase.lbl.gov. Currently, the database content is derived from more than 4000 relevant articles describing over 9000 experiments in relation to 155 microbes. It contains data on the regulation of ~;14000 genes and evidence for ~;7500 interactions with ~;850 regulators. RegTransBase additionally provides an expertly curated library of alignments of known transcription factor binding sites covering a wide range of bacterial species. Each alignment contains information as to the transcription factor which binds the DNA sequence, the exact location of the binding site on a published genome, and links to published articles. RegTransBase builds upon these alignments by containing a set of computational modules for the comparative analysis of regulons among related organisms. These modules guide a user through the appropriate steps of transferring known or high confidence regulatory binding site results to other microbial organisms, allowing them to study many organisms at one time, while warning of analysis possibly producing low confidence results, and providing them with sound default parameters. There is an increasingly tight coupling of RegTransBase with MicrobesOnline in reporting cis-regulatory sites and regulatory interactions, and integrating RegTransBase searches into MicrobesOnLine cart functions.

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