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RegTransBase


NAR Molecular Biology Database Collection entry number 947
Kazakov A.E.1, Cipriano M.J.2, Novichkov P.S.3,4, Minovitsky S.2, Vinogradov D.V.1, Arkin A.2,4,5,6, Mironov A.A.1,7,8, Gelfand M.S.1,7,8,10, Dubchak I.2,9,10
1Institute for Information Transmission Problems RAS, Bolshoi Karetny pereulok 19, Moscow 127994, Russia
2Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
3National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
4Howard Hughes Medical Institute, Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
5Department of Bioengineering, University of California, Berkeley, CA 94710, USA
6Virtual Institute of Microbial Stress and Survival, Berkeley, CA 94710, USA
7Faculty of Bioengineering and Bioinformatics, Moscow State University. Vorobievy Gory 1-73, Moscow 119992, Russia
8State Research Center GosNIIGenetika. 1-j Dorozhny proezd 1, Moscow, 117545, Russia
9Department of Energy Joint Genome Institute, 2800 Mitchell Drive,Walnut Creek, CA 94598, USA

Database Description

RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data: the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein, and characterization of regulatory mutations.

Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species.

Acknowledgements

Creation of RegTransBase was partially supported by the Howard Hughes Medical Institute (grant 55005610), INTAS (grant 05-1000008-8028), Russian Academy of Sciences (Program "Molecular and Cellular Biology"), Integrated Genomics, Inc. This work was part of the Virtual Institute for Microbial Stress and Survival (http://VIMSS.lbl.gov) supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Program:GTL through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy.

References

Kazakov A.E., Cipriano M.J., Novichkov P.S., Minovitsky S., Vinogradov D.V., Arkin A.P., Mironov A.A., Gelfand M.S. and Dubchak I. (2007) RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res., 35: in press.


Go to the abstract in the NAR 2007 Database Issue.
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