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NAR Molecular Biology Database Collection entry number 623
Misra R.V.1, Horler R.S.P.1, Reindl W.1, Goryanin I.I.2 and Thomas G.H.1
1Department of Biology (Area 10), University of York, PO Box 373,York, YO10 5YW, UK
2Scientific Computing and Mathematical Modelling, GlaxoSmithKline, Gunnels Wood Road, Stevenage, UK, SG1 2NY

Database 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 Developments

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.


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.

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