Cipriano, Michael J;
Novichkov, Pavel N;
Kazakov, Alexey E;
Rodionov, Dmitry A;
Arkin, Adam P;
Gelfand, Mikhail S;
Dubchak, Inna
RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
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Media type:
E-Article
Title:
RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
Contributor:
Cipriano, Michael J;
Novichkov, Pavel N;
Kazakov, Alexey E;
Rodionov, Dmitry A;
Arkin, Adam P;
Gelfand, Mikhail S;
Dubchak, Inna
Published:
Springer Science and Business Media LLC, 2013
Published in:
BMC Genomics, 14 (2013) 1
Language:
English
DOI:
10.1186/1471-2164-14-213
ISSN:
1471-2164
Origination:
Footnote:
Description:
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.