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. 2013 Apr 2:14:213.
doi: 10.1186/1471-2164-14-213.

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

Michael J Cipriano  1 , Pavel N Novichkov, Alexey E Kazakov, Dmitry A Rodionov, Adam P Arkin, Mikhail S Gelfand, Inna Dubchak
Affiliations

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

Michael J Cipriano et al. BMC Genomics. .

Abstract

Background: Due to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly remains a field of semi-manual examination since absence of a knowledgebase and informatics platform for automated and systematic investigation restricts opportunities for computational prediction. Additionally, confirming computationally inferred regulons by experimental data is critically important.

Description: RegTransBase is an open-access platform with a user-friendly web interface publicly available at http://regtransbase.lbl.gov. It consists of two databases - a manually collected hierarchical regulatory interactions database based on more than 7000 scientific papers which can serve as a knowledgebase for verification of predictions, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools. RegTransBase captures the knowledge from published scientific literature using controlled vocabularies and contains various types of experimental data, such as: the activation or repression of transcription by an identified direct regulator; determination of the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA; mapping of binding sites for a regulatory protein; characterization of regulatory mutations. Analysis of the data collected from literature resulted in the creation of Putative Regulons from Experimental Data that are also available in RegTransBase.

Conclusions: RegTransBase is a powerful user-friendly platform for the investigation of regulation in prokaryotes. It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation of transcriptional regulation data.

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Figures

Figure 1
Figure 1
Home page of RegTransBase. Data navigation panel with its major classifications in the middle of the page.
Figure 2
Figure 2
Step-by-step data navigation in search for the experiments where cis-elements are involved in the fructose-dependent regulation.
Figure 3
Figure 3
Access to the RegTransBase PWMs and browsing capabilities.
See this image and copyright information in PMC

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