BMC Genomics Database DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions Jingkai Yu1, Svetlana Pacifico1, Guozhen Liu1 and Russell L Finley Jr*1,2 BioMed Central Open Access Address: 1Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield Ave., Detroit, MI 48201, USA and 2Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 East Canfield Ave., Detroit, MI 48201, USA Email: Jingkai Yu - jingkai@wayne.edu; Svetlana Pacifico - lpacifico@wayne.edu; Guozhen Liu - gzliu@supperarray.net; Russell L Finley* - rfinley@wayne.edu * Corresponding author Published: 7 October 2008 BMC Genomics 2008, 9:461 doi:10.1186/1471-2164-9-461 This article is available from: http://www.biomedcentral.com/1471-2164/9/461 Received: 13 May 2008 Accepted: 7 October 2008 © 2008 Yu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi- organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. Description: DroID, the Drosophila Interactions Database, is a comprehensive interactions database designed specifically for Drosophila. DroID houses published physical protein interactions, genetic interactions, and computationally predicted interactions, including interologs based on data for other model organisms and humans. All interactions are annotated with original experimental data and source information. DroID can be searched and filtered based on interaction information or a comprehensive set of gene attributes from Flybase. DroID also contains gene expression and expression correlation data that can be searched and used to filter datasets, for example, to focus a study on sub-networks of co-expressed genes. To address the inherent noise in interaction data, DroID employs an updatable confidence scoring system that assigns a score to each physical interaction based on the likelihood that it represents a biologically significant link. Conclusion: DroID is the most comprehensive interactions database available for Drosophila. To facilitate downstream analyses, interactions are annotated with original experimental information, gene expression data, and confidence scores. All data in DroID are freely available and can be searched, explored, and downloaded through three different interfaces, including a text based web site, a Java applet with dynamic graphing capabilities (IM Browser), and a Cytoscape plug-in. DroID is available at http://www.droidb.org. Page 1 of 9 (page number not for citation purposes)