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RegulonDB


NAR Molecular Biology Database Collection entry number 116
Salgado, H, Gama-Castro, S., MartÍnez-Antonio, A., DÍaz-Peredo, E., SÁnchez-Solano, F., GarcÍa-Alonso, D., Peralta-Gil, M., Santos-Zavaleta, A., JimÉnez-Jacinto, V., Collado-Vides, J.
Program of Computational Genomics, CIFN, UNAM A.P. 565-A Cuernavaca, Morelos, 62100, Mexico

Database Description

RegulonDB is a database on mechanisms of transcription regulation, operon organization and knowledge on physiological conditions under which genes are induced or repressed in Escherichia coli K-12. The current version has an important increase in all objects of the database, regulons, operons, promoters, binding sites, regulatory proteins, their allosteric conformations, and terminators. It also has novel information about affected genes and the associated conditions of growth of E. coli, even if in many cases very little is known about the regulatory mechanism. Furthermore, a major improvement is a graphical display enabling browsing of the database with a Java-based interactive interface with three zoom-levels connected to properties of each chromosomal element. RegulonDB can be accessed on the web at http://www.cifn.unam.mx/Computational_Genomics/regulondb/.

Recent Developments

Information of the effect in the expression of specific genes when changing the growth conditions of the cell, as well as experiments studying the effects of mutating regulatory genes was added recently. Alignments and matrixes for the transcriptional regulators were updated and a new tool for searching regulatory binding sites is available. Also RegulonDB has a new interface and graphical tools.

Acknowledgements

This work was supported by NIH grants GM62205-02 and 1-R01-RR07861. We acknowledge Rosa MarÍa GutiÉrrez-Rios and MÓnica PeÑaloza-SpÍnola their participation in discussions on growth conditions, and , CÉsar Bonavides-MartÍnez, VÍctor del Moral and Romualdo Zayas for their computer support.

References

1. MartÍnez-Antonio,A., Salgado,H., Gama-Castro,S., GutiÉrrez-RÍos,R.M., JimÉnez-Jacinto, V., and Collado-Vides, J. (2003) Environmental Conditions and Transcriptional Regulation in Escherichia coli: A Physiological Integrative Approach. Biotechnol & Bioeng. In press.
2. GutiÉrrez-RÍos,R.M., Rosenblueth,D.A., Loza,J.A., Huerta,A., Glasner,J.D., Blattner,F. and Collado-Vides J. (2003) Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles. Genome Res. In press.
3. MartÍnez-Antonio,A., and Collado-Vides,J. (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol, Oct 6(5): In press
4. Huerta, A.M., Glasner,J.D., Jin, H., Blattner, F.D., GutiÉrrez-RÍos, R.M. and Collado-Vides,J. (2002) GETools: Gene Expression Tool for Analysis of Transcriptome Experiments in Escherichia coli. TIGS 18,217-218.
5. Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., MillÁn-ZÁrate,D., DÍaz-Peredo,E., SÁnchez-Solano, F., PÉrez-Rueda,E., Bonavides-MartÍnez,C. and Collado-Vides J.(2001) RegulonDB (version 3.2): Transcriptional Regulation and Operon Organization in Escherichia coli K-12. Nucleic Acids Res., 29,72-74.
6. Salgado,H., Moreno-Hagelsieb,G., Smith,T.F. and Collado-Vides J. (2000) Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. USA, 97(12),6652-6657.
7. PÉrez-Rueda,E. and Collado-Vides J. (2000) The Repertoire of DNA-Binding Transcriptional Regulators in Escherichia coli. Nucleic Acids Res., 28,1838-1847.
8. Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., MillÁn-ZÁrate,D., Blattner,F.R. and Collado-Vides J. (2000) RegulonDB (version 3.0): Transcriptional Regulation and Operon Organization in Escherichia coli. Nucleic Acids Res., 28,65-67.
9. Salgado,H., Santos,A., Garza-Ramos,U., van Helden,J., DÍaz,E. and Collado-Vides J. (1999). RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res., 27(1),59-60.
10. Thieffry,D., Salgado, H., Huerta,A.M. and Collado-Vides,J. (1998) Prediction of transcription regulatory sites in the complete genome of Escherichia coli. Bioinformatics,14(5),391-400.
11. Huerta,A.M., Salgado,H., Thieffry,D. and Collado-Vides J. (1998) RegulonDB: A Database on Transcription Regulation in Escherichia coli. Nucleic Acids Res. 26, 55-60.


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