RegTransBase--a Database of Regulatory Sequences and Interactions in a Wide Range of Prokaryotic Genomes

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Dec 5

PMID 17142223

Citations 55

Authors

Alexei E Kazakov

Michael J Cipriano

Pavel S Novichkov

Simon Minovitsky

Dmitry V Vinogradov

Adam Arkin

Andrey A Mironov

Mikhail S Gelfand

Inna Dubchak

Affiliations

Soon will be listed here.

Abstract

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. RegTransBase is available at http://regtransbase.lbl.gov.

Citing Articles

Revealing 29 sets of independently modulated genes in , their regulators, and role in key physiological response.

Poudel S, Tsunemoto H, Seif Y, Sastry A, Szubin R, Xu S Proc Natl Acad Sci U S A. 2020; 117(29):17228-17239.

PMID: 32616573 PMC: 7382225. DOI: 10.1073/pnas.2008413117.

The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of subsp. and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator.

Shyntum D, Nkomo N, Shingange N, Gricia A, Bellieny-Rabelo D, Moleleki L Front Microbiol. 2019; 10:2379.

PMID: 31681235 PMC: 6813493. DOI: 10.3389/fmicb.2019.02379.

The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database.

Paley S, Karp P BMC Bioinformatics. 2019; 20(1):399.

PMID: 31319812 PMC: 6637615. DOI: 10.1186/s12859-019-2971-6.

Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa.

Khademi S, Sazinas P, Jelsbak L Genome Biol Evol. 2019; 11(5):1385-1397.

PMID: 30980662 PMC: 6505451. DOI: 10.1093/gbe/evz083.

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis.

Chen X, Ma A, McDermaid A, Zhang H, Liu C, Cao H Genes (Basel). 2018; 9(6).

PMID: 29849014 PMC: 6027394. DOI: 10.3390/genes9060278.

References

Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E . PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 2003; 31(1):266-9. PMC: 165484. DOI: 10.1093/nar/gkg037. View

Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides N . The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 2005; 34(Database issue):D332-4. PMC: 1347507. DOI: 10.1093/nar/gkj145. View

Makita Y, Nakao M, Ogasawara N, Nakai K . DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 2003; 32(Database issue):D75-7. PMC: 308808. DOI: 10.1093/nar/gkh074. View

Crooks G, Hon G, Chandonia J, Brenner S . WebLogo: a sequence logo generator. Genome Res. 2004; 14(6):1188-90. PMC: 419797. DOI: 10.1101/gr.849004. View

Frazer K, Pachter L, Poliakov A, Rubin E, Dubchak I . VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004; 32(Web Server issue):W273-9. PMC: 441596. DOI: 10.1093/nar/gkh458. View

Yellaboina S, Seshadri J, Kumar M, Ranjan A . PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Nucleic Acids Res. 2004; 32(Web Server issue):W318-20. PMC: 441502. DOI: 10.1093/nar/gkh364. View

Robison K, McGuire A, Church G . A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol. 1998; 284(2):241-54. DOI: 10.1006/jmbi.1998.2160. View

Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A . RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 2005; 34(Database issue):D394-7. PMC: 1347518. DOI: 10.1093/nar/gkj156. View

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R . ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. BMC Microbiol. 2006; 6:29. PMC: 1453763. DOI: 10.1186/1471-2180-6-29. View

10.

Markowitz V, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A . The integrated microbial genomes (IMG) system. Nucleic Acids Res. 2005; 34(Database issue):D344-8. PMC: 1347387. DOI: 10.1093/nar/gkj024. View

11.

Martinez-Bueno M, Molina-Henares A, Pareja E, Ramos J, Tobes R . BacTregulators: a database of transcriptional regulators in bacteria and archaea. Bioinformatics. 2004; 20(16):2787-91. DOI: 10.1093/bioinformatics/bth330. View

12.

Pruitt K, Tatusova T, Maglott D . NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2004; 33(Database issue):D501-4. PMC: 539979. DOI: 10.1093/nar/gki025. View

13.

Gonzalez A, Espinosa V, Vasconcelos A, Perez-Rueda E, Collado-Vides J . TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Res. 2004; 33(Database issue):D98-102. PMC: 540008. DOI: 10.1093/nar/gki054. View

14.

Alm E, Huang K, Price M, Koche R, Keller K, Dubchak I . The MicrobesOnline Web site for comparative genomics. Genome Res. 2005; 15(7):1015-22. PMC: 1172046. DOI: 10.1101/gr.3844805. View

15.

Munch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M . Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics. 2005; 21(22):4187-9. DOI: 10.1093/bioinformatics/bti635. View

16.

Wheeler D, Barrett T, Benson D, Bryant S, Canese K, Chetvernin V . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2005; 34(Database issue):D173-80. PMC: 1347520. DOI: 10.1093/nar/gkj158. View

17.

Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C . The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002; 12(10):1611-8. PMC: 187536. DOI: 10.1101/gr.361602. View

18.

Stein L, Mungall C, Shu S, Caudy M, Mangone M, Day A . The generic genome browser: a building block for a model organism system database. Genome Res. 2002; 12(10):1599-610. PMC: 187535. DOI: 10.1101/gr.403602. View

19.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View