RT Journal Article
T1 EcID: a database for the inference of functional interactions in E. coli
A1 Andrés León, Eduardo
A1 Ezkurdia, Iakes
A1 García-Jiménez, Beatriz
A1 Valencia, Alfonso
A1 Juan, David
AB 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.
PB Oxford University Press
SN 0305-1048 (print)
SN 1362-4962 (online)
YR 2009
FD 2009-01
LK https://hdl.handle.net/10016/9716
UL https://hdl.handle.net/10016/9716
LA eng
NO EC [LSHG-CT-2003-503265 (BioSapiens) and LSHG-CT-2004-512092 (EMBRACE)]. Funding for open access charge: European Union.
DS e-Archivo
RD 19 may. 2024