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Curated experimental and bioinformatic information about E. coli genes and gene products
EchoBASE curates experimental and bioinformatic information about E. coli genes and their gene products. The aim of this database is to provide information that will lead to functional predictions for gene products of unknown function. EchoBASE is part of the International E. coli Alliance.
As of July 11, 2006, there are 303 curated references in EchoBASE. The database contains descriptions of papers with information on the function of individual gene products, as well as the actual data from larger, post-genomic studies, which can be searched and manipulated. There are 106 curated experiments which are grouped by type: Biochemistry (10), Bioinformatics (11), Genetics (13), Microarray (6), Protein-Protein Interaction (3), Proteomics (15), Structure (46), and Transcript Level (2).
Other features of EchoBASE are Orphan Enzymes (>90 enzyme activities that have been measured in E. coli, but not mapped to a gene product or gene), EchoABC (a comprehensive list of ABC transporters with links to references and structures, if known), EchoLOCATION (experimentally determined or predicted subcellular location of E. coli products), and EchoPDB (a list of all known structures for E. coli proteins with links to references and the PDB).
The curated experimental datasets can be browsed by experiment type.
EchoBASE can be searched by gene name. The results page for a gene name search contains the ECK no., synonyms, known or predicted function of the gene product, links to the DNA and protein sequences, position on the genome, a map with approx. 5 kb of flanking DNA, links to the gene in other databases, and a list of the experiments where the gene, its transcript, or product was detected with links to the data.
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- Horler, RS et al. (2009) EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations. Bioinformatics 25 163-6 PubMed
Thomas, G.H. (1999) Completing the E. coli proteome: a database of gene products characterised since completion of the genome sequence. Bioinformatics 15:860-861.
Misra, R.V. et al. (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 33(Database issue):D329-33