BMC Genomics 2008, 9:461 http://www.biomedcentral.com/1471-2164/9/461 some features especially geared toward researchers (Figure 1). Drosophila DroID is an extensive update of an earlier database [28]. New features that are described in more detail below include a web interface, gene expression data, calculated gene correlation values, confidence scores, and substan- tially more interaction data. In addition, DroID is updated quarterly and each version is available for down- load. The current version of DroID (v4.0) is described here. Interaction data and generation of interologs DroID is stored in a relational database with each major interaction dataset corresponding to one database table (see Table 1). As new datasets become available, new tables are added. The different datasets can be seamlessly integrated or searched separately. Frequently, the overlap among different datasets contains more reliable interac- tions, and this overlap will be obvious to users. While much of the data in DroID represents protein-protein interactions, all interactions are keyed to gene or locus identifiers because protein interaction data rarely includes knowledge of specific alternative splice forms or protein isoforms. DroID uses the Flybase gene number (FBgn) to specify a gene or a protein encoded by a gene. Other com- mon gene identifiers, such as the gene symbol or CG number, are also stored. A C B D FDirgouIDrea1ccess interfaces DroID access interfaces. (A) DroID search page; (B) Interaction search results page from which results can be filtered using gene expression data or confidence scores; (C) Cytoscape plug-in, which queries DroID directly and enables network visualiza- tion and analysis within Cytoscape; (D) IM Browser interface with dynamic graphing capabilities. All interfaces can be accessed from http://www.droidb.org. Page 3 of 9 (page number not for citation purposes)