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Bacteriome.org

http://www.bacteriome.org/

Description :
Protein interaction database for E. coli

Open Proteomics Database

http://bioinformatics.icmb.utexas.edu/OPD/

Description :
Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium

E. coli Genome Project

http://www.genome.wisc.edu/

Description :
U.Washington E. coli genome project site maintains and updates the annotated sequence of the E. coli K12 genome; also has resources and tools for functional characterization of E. coli genes

E.Coli Index

http://ecoli.bham.ac.uk/

Description :
comprehensive guide to information relating to E. coli; home of Echobase: a database of E. coli genes characterized since the completion of the genome

DPInteract

http://arep.med.harvard.edu/dpinteract/

Description :
Binding sites for E. coli DNA-binding proteins

References :
1. Robison K, McGuire AM, Church GM. 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: 241-254.

RegulonDB

http://regulondb.ccg.unam.mx/

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 develoments :
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.

Aknowledgement :
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.

TRACTOR db

http://www.tractor.lncc.br/

Description :
Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, Transcription Factors (TFs), TFs' binding sites, operons) within its genome. As more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcriptional regulation. In this work we present TRACTOR_DB (TRAnscription FaCTORsÿ predicted sites in prokaryotic genomes), a relational database that contains computational predictions of new members of 74 regulons in eight gamma-proteobacterial genomes. To produce these predictions we used a comparative genomics approach of which several proof-of-principle articles for large regulons have been published. Furthermore, we used the predictions stored in our database to assess the conservation of regulons' size across all the eight genomes and showed that a correlation exists between the conservation of a regulatory site and the structure of the Transcription Unit (TU) it regulates. TRACTOR_DB may be currently accessed at http://www.bioinfo.cu/database, http://www.tractor.lncc.br or at http://www.cifn.unam.mx/Computational_Genomics/.

EchoBASE

http://www.ecoli-york.org/

Description :
EchoBASE is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. Its aim is to collate information from a wide range of sources to provide clues to the functions of the approximately 1500 gene products that have no confirmed cellular function. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and associates experimental data with the E. coli genes and their products. Experiments that can be held within EchoBASE include proteomics studies, microarray data, protein-protein interaction data, structural data and bioinformatic studies. Proteomics studied of E. coli are well covered in the database and complex queries can be made to establish the totality of the experimentally determined proteome, or of particular sub-proteome. Validation of FUN gene products by proteomics is an important criterion in choosing which to study and EchoBASE currently has data for 254 FUN genes whose synthesis has been confirmed experimentally. EchoBASE also contains annotated information on 'orphan' enzyme activities from this microbe to aid characterisation of the proteins that catalyse these elusive biochemical reactions.

Recent develoments :
EchoBASE is a new database that was launched in February 2004 and has been updated with version 1.1 in May and later with version 1.2 in September 2004. Further version improvements will be made on a 6 monthly basis, but data is being continually curated into the database which can be followed in the 'What's new' page.

Aknowledgement :
We would like to acknowledge CNAP and the University of York for technical support and hosting EchoBASE, and thank GlaxoSmithKline and the British Biotechnology and Biological Sciences Research Council for financial support.

ASAP - A Systematic Annotation Package

https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm

Description :
Community analysis of E. coli and related genomes

CCDB - The CyberCell Database

http://redpoll.pharmacy.ualberta.ca/CCDB

Description :
E. coli database at U. Alberta

coliBase

http://colibase.bham.ac.uk/

Description :
A database for E. coli, Salmonella and Shigella

EcoCyc

http://ecocyc.org/

Description :
EcoCyc is a model organism database that describes the genome and the biochemical network of E. coli K-12. EcoCyc version 12.1 (June 2008) integrates the annotated E. coli genome sequence with a rich collection of information curated from more than 17,000 publications. The database describes each E. coli gene and its gene product. The EcoCyc project closely monitors the biochemical literature and incorporates newly determined E. coli gene functions into EcoCyc. Metabolic and signaling pathways are described as interconnected sets of biochemical reactions. Transport processes are encoded as reactions whose substrates are labeled with the compartments they span. Mechanisms of gene regulation are also encoded as sequences of molecular interactions, such as binding of a transcription factor to its complementary DNA site. EcoCyc users employ the Pathway Tools software to query and visualize information within EcoCyc. The software produces intuitive drawings of pathways, operons, biochemical reactions, transport processes, and includes a genome browser. The software also produces visualizations of the entire metabolic map and regulatory network of E. coli. Gene expression and other omics datasets can be painted onto those diagrams for analysis. EcoCyc is available through the WWW at the URL provided. It is also available as a binary program for local installation on the Macintosh, PC, and Linux, and as a set of flat files.

Recent develoments :
A PC version of EcoCyc is now available. Extensive new information on transcriptional regulation of gene expression has been added in the last year.

Aknowledgement :
This work was supported by grant GM077678 from the National Institutes of Health.

EcoGene

http://ecogene.org/

Description :
The EcoGene database provides a set of gene and protein sequences derived from the genome sequence of Escherichia coli K-12. EcoGene is a source of re-annotated sequences for the SWISS-PROT and Colibri databases. EcoGene is used for genetic and physical map compilations in collaboration with the Coli Genetic Stock Center. The EcoGene13 release (October, 2000) includes 4295 genes. EcoGene13 differs from the Genbank annotation of the complete genome sequence (in U00096) in several ways, including (1) the revision of 717 predicted or confirmed gene start sites, (2) the correction or hypothetical reconstruction of 61 frameshifts caused by either sequence error or mutation, (3) the reconstruction of 14 protein sequences interrupted by the insertion of IS elements, and (4) predictions that 92 genes are partially deleted gene fragments. A literature survey identified 810 proteins whose N-terminal amino acids have been verified by protein sequencing. 21,899 gene-citation cross-references to 8,552 literature citations, with links to Medline abstracts, are provided. EcoGene is accessible through a WWW interface: http://bmb.med.miami.edu/EcoGene/EcoWeb. Users can search and retrieve information from a set of 4295 individual EcoGene GenePage HTML files. Alternatively, users can download various complete text-based genome-scale datasets including DNA sequences, protein sequences, genome sequence gene positions, database cross-references and descriptive annotation. These datasets can be easily imported into database management systems and should facilitate various genome-scale computational and functional analysis projects. In addition, a database of intergenic DNA sequences, including genome positions for a number of novel or previously characterized intergenic repeat DNA family members is provided.

Essential genes in E. coli

http://www.genome.wisc.edu/resources/essential.htm

Description :
First results of an E. coli gene deletion project

GenoBase

http://ecoli.aist-nara.ac.jp/

Description :
E. coli genome database at Nara Institute

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