EcID: a database for the inference of functional interactions in E. coli

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dc.contributor.author Andrés León, Eduardo
dc.contributor.author Ezkurdia, Iakes
dc.contributor.author García-Jiménez, Beatriz
dc.contributor.author Valencia, Alfonso
dc.contributor.author Juan, David
dc.date.accessioned 2010-11-29T12:07:10Z
dc.date.available 2010-11-29T12:07:10Z
dc.date.issued 2009-01
dc.identifier.bibliographicCitation Nucleic acids research, vol. 37, suppl. 1 (Jan. 2009), p.629-635
dc.identifier.issn 0305-1048 (print)
dc.identifier.issn 1362-4962 (online)
dc.identifier.uri http://hdl.handle.net/10016/9716
dc.description.abstract The EcID database (Escherichia coli Interaction Database) provides a framework for the integration of information on functional interactions extracted from the following sources: EcoCyc (metabolic pathways, protein complexes and regulatory information), KEGG (metabolic pathways), MINT and IntAct (protein interactions). It also includes information on protein complexes from the two E. coli high-throughput pull-down experiments and potential interactions extracted from the literature using the web services associated to the iHOP text-mining system. Additionally, EcID incorporates results of various prediction methods, including two protein interaction prediction methods based on genomic information (Phylogenetic Profiles and Gene Neighbourhoods) and three methods based on the analysis of co-evolution (Mirror Tree, In Silico 2 Hybrid and Context Mirror). EcID associates to each prediction a specifically developed confidence score. The two main features that make EcID different from other systems are the combination of co-evolution-based predictions with the experimental data, and the introduction of E. colispecific information, such as gene regulation information from EcoCyc. The possibilities offered by the combination of the EcID database information are illustrated with a prediction of potential functions for a group of poorly characterized genes related to yeaG. EcID is available online at http:// ecid.bioinfo.cnio.es.
dc.description.sponsorship EC [LSHG-CT-2003-503265 (BioSapiens) and LSHG-CT-2004-512092 (EMBRACE)]. Funding for open access charge: European Union.
dc.format.mimetype text/plain
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.rights © 2008 The Author(s)
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.title EcID: a database for the inference of functional interactions in E. coli
dc.type article
dc.relation.publisherversion http://dx.doi.org/10.1093/nar/gkn853
dc.subject.eciencia Informática
dc.identifier.doi 10.1093/nar/gkn853
dc.rights.accessRights openAccess
dc.identifier.publicationfirstpage 629
dc.identifier.publicationissue 1
dc.identifier.publicationlastpage 635
dc.identifier.publicationtitle Nucleic acids research
dc.identifier.publicationvolume 37
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