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

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dc.affiliation.dptoUC3M. Departamento de Informáticaes
dc.affiliation.grupoinvUC3M. Grupo de Investigación: Laboratorio de Control, Aprendizaje y Optimización de Sistemas (CAOS)es
dc.contributor.authorAndrés León, Eduardo
dc.contributor.authorEzkurdia, Iakes
dc.contributor.authorGarcía-Jiménez, Beatriz
dc.contributor.authorValencia, Alfonso
dc.contributor.authorJuan, David
dc.date.accessioned2010-11-29T12:07:10Z
dc.date.available2010-11-29T12:07:10Z
dc.date.issued2009-01
dc.description.abstractThe 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.sponsorshipEC [LSHG-CT-2003-503265 (BioSapiens) and LSHG-CT-2004-512092 (EMBRACE)]. Funding for open access charge: European Union.
dc.format.mimetypetext/plain
dc.format.mimetypeapplication/pdf
dc.identifier.bibliographicCitationNucleic acids research, vol. 37, suppl. 1 (Jan. 2009), p.629-635
dc.identifier.doi10.1093/nar/gkn853
dc.identifier.issn0305-1048 (print)
dc.identifier.issn1362-4962 (online)
dc.identifier.publicationfirstpage629
dc.identifier.publicationissue1
dc.identifier.publicationlastpage635
dc.identifier.publicationtitleNucleic acids research
dc.identifier.publicationvolume37
dc.identifier.urihttps://hdl.handle.net/10016/9716
dc.language.isoeng
dc.publisherOxford University Press
dc.relation.publisherversionhttp://dx.doi.org/10.1093/nar/gkn853
dc.rights© 2008 The Author(s)
dc.rights.accessRightsopen access
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.subject.ecienciaInformática
dc.titleEcID: a database for the inference of functional interactions in E. coli
dc.typeresearch article*
dspace.entity.typePublication
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