title: EcID. A database for the inference of functional interactions in E. coli.
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. coli-specific 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.
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre-CNIO and Computer Sciences Department, Universidad Carlos III de Madrid, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Andres Leon
authors.forename: Iakes
authors.initials: I
authors.lastname: Ezkurdia
authors.forename: Beatriz
authors.initials: B
authors.lastname: García
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.forename: David
authors.initials: D
authors.lastname: Juan
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D025941:Protein Interaction Mapping; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D029968:Escherichia coli Proteins