EchoBASE: Difference between revisions
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Raju Misra | *Raju Misra | ||
*Richard Horler | |||
*Gavin Thomas | |||
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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). | 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), and EchoPDB (a list of all known structures for E. coli proteins with links to references and the PDB). | 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]] | [[Category:E. coli protein localization]] | ||
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=References= | =References= | ||
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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. | 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 | 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= | =External Links= | ||
[http://ecoli-york.org {{PAGENAME}}] | [http://ecoli-york.org {{PAGENAME}}] | ||
==Discussion of {{PAGENAME}} on other websites== | ==Discussion of {{PAGENAME}} on other websites== | ||
Latest revision as of 00:11, 23 May 2010
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.
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| What: |
Curated experimental and bioinformatic information about E. coli genes and gene products |
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| Upcoming events: | |
| Web Services: |
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| edit table |
About EchoBASE
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.
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), EchoLOCATION (experimentally determined or predicted subcellular location of E. coli products[1]), and EchoPDB (a list of all known structures for E. coli proteins with links to references and the PDB).
Using EchoBASE
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.
Technology
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
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