EchoBASE: an integrated post-genomic database for Escherichia coli

Abstract

EchoBASE (http://www.ecoli-york.org) 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 the association of 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 bioinformatics studies. EchoBASE also contains annotated information on 'orphan' enzyme activities from this microbe to aid characterization of the proteins that catalyse these elusive biochemical reactions.

Figure 1

Screenshot of the EchoBASE gene page for cueO. The gene and protein sequence are linked from the gene name (top box). There are a number of different experiments associated with this gene and information for a proteomics experiment by Link et al. is displayed (top right box). This is the experiment overview page, with details of the experiment and our basic comment, and below this are the options for displaying different subsets of the data from this paper and to rank this by particular properties. Specific information in this paper that relates to CueO can be viewed in detail by following another link which includes our full annotation of the papers and all relevant information for the selected gene (right box).

Figure 2

Screenshot of the EchoORPHAN page from the database. The initial page displays the ‘Enzyme rating’, its current status and the EC code linking to BRENDA (14). This ranked list is superimposed with the detail page for the orphan enzyme aminobutyraldehyde dehydrogenase which was our highest scoring orphan enzyme and has recently been mapped to the ydcW gene product.