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APID: Agile Protein Interaction DataAnalyzer
Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CIC, CSIC/USAL) 37007 Salamanca, Spain
*To whom correspondence should be addressed. Tel.: +34 923 294819; Fax: +34 923 294743; Email: jrivas{at}usal.es
Received February 14, 2006. Revised February 23, 2006. Accepted March 14, 2006.
Agile Protein Interaction DataAnalyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein–protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore >35 000 different proteins and 111 000 different proven interactions. The web includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Such parameters are for the ‘proteins’: connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; and for the ‘interactions’: number of methods, GO overlapping, iPfam domain–domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. The application is available open access at http://bioinfow.dep.usal.es/apid/.
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