View source for EchoBASE

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[[Category:Databases]]
[[Category:E. coli Databases]]
[[Category:IECA Portal]]
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!align=left {{table heading style}} |Link/URL:
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[http://www.ecoli-york.org/ EchoBASE]
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!align=left {{table heading style}} |What:
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Curated experimental and bioinformatic information about E. coli genes and gene products
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!align=left {{table heading style}} |Who:
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*Raju Misra
*Richard Horler
*Gavin Thomas 
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!align=left {{table heading style}} |Updates:
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!align=left {{table heading style}} |Upcoming events:
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!align=left {{table heading style}} |Web Services:
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=About {{PAGENAME}}=
[http://ecoli-york.org {{PAGENAME}}] 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. ''Echo''BASE is part of the [http://www.uni-giessen.de/~gx1052/IECA/ieca.html International ''E. coli'' Alliance].

=Content=
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), [http://www.york.ac.uk/res/thomas/echolocadv.cfm EchoLOCATION] (experimentally determined or predicted subcellular location of ''E. coli'' products<ref name='PMID:19015139'/>), and EchoPDB (a list of all known structures for E. coli proteins with links to references and the PDB).

[[Category:E. coli protein localization]]

=Using {{PAGENAME}}=  

==Browsing==
The curated experimental datasets can be browsed by experiment type.

==Searching==
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.
  
==Usage examples==

''Add links to additional pages describing success stories here.''

=Other sites with related content=

=Technology=

==Web Services/API==

=Discussion=



=References=
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<references />
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
=External Links=
[http://ecoli-york.org {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==