Open Access Highly Accessed Database

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

Michael J Cipriano1, Pavel N Novichkov2, Alexey E Kazakov2, Dmitry A Rodionov34, Adam P Arkin25, Mikhail S Gelfand46 and Inna Dubchak27*

Author Affiliations

1 Department of Microbiology, University of California Davis, Davis, CA, 95616, USA

2 Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA

3 Sanford-Burnham Medical Research Institute, La Jolla, CA, 92037, USA

4 A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia

5 Department of Bioengineering, University of California, Berkeley, CA, 94720, USA

6 M.V. Lomonosov Moscow State University, Vorobyevy Gory 1073,, Moscow, 119991, Russia

7 Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA

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BMC Genomics 2013, 14:213  doi:10.1186/1471-2164-14-213

Published: 2 April 2013

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 webcite. 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.

Keywords:
Transcriptional regulation; Prokaryotes; Comparative genomics