DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions.
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.


METHODS
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.


CONCLUSIONS
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.
Yu
Jingkai
J
Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield Ave., Detroit, MI 48201, USA. jingkai@wayne.edu
Pacifico
Svetlana
S
Liu
Guozhen
G
Finley
Russell L
RL
D000818:Animals; D003628:Database Management Systems; D030541:Databases, Genetic; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics*; D015870:Gene Expression; D017344:Genes, Insect; D025941:Protein Interaction Mapping / Q000379:methods*; D014584:User-Computer Interface
D029721:Drosophila Proteins