BMC Genomics 2008, 9:461 http://www.biomedcentral.com/1471-2164/9/461 n o i t a l e r r o c n o i s s e r p x E Yeast two-hybrid data Predicted interologs FGiegnuerex3pression correlation for interaction data sets in DroID Gene expression correlation for interaction data sets in DroID. Boxplots of correlation distributions of different data sets show that all sets of interactions in DroID have higher average expression correlation than the set of random protein pairs. The X-axis represents various sets of interactions in DroID, 'Random' denotes sets of random protein pairs. The Y-axis represents expression correlations. tion data that are currently available come from studies that are independent of gene expression. Examples include yeast two-hybrid data in which pairs of proteins are expressed together in yeast, whether or not they are co- expressed in vivo, and co-AP experiments in which often at least one of the proteins is artificially expressed with an affinity tag in tissue culture cells. Thus, the protein inter- actions in DroID and most other databases represent pairs of proteins that may interact in vivo, but only if they are expressed together. A powerful way to view this interac- tion data, therefore, is in the context of gene expression patterns for a particular tissue or developmental time point. DroID includes gene expression data from genome- wide developmental studies. This data can be used to con- strain a set of interactions to include only genes expressed at a user-defined level and time point or developmental stage. DroID access interfaces All data in DroID can be accessed and downloaded in part or whole via three different interfaces (Figure 1). A user- friendly web interface is provided for simple searching, browsing, and downloading of DroID data. Going to the DroID web page opens a search box, which asks users for a term describing a gene or protein. The term can be a gene symbol, name, synonym, or a term describing a gene or protein (Figure 1A). Clicking 'Search Genes' produces a page listing genes that fit the search criteria. On this page, users select one or any number of the genes, and then have the option to select specific interaction datasets or to search all of them simultaneously. The search produces a results page listing the found interactions and their cur- rent confidence scores (Figure 1B). Each interaction is rep- resented by the symbols of the two genes and a list of the datasets in which they were found. Additional informa- tion about each gene, including GO annotations and links to Flybase can be obtained by clicking on the gene sym- bol. Similarly, clicking on the dataset name for each inter- action reveals its details, including original experimental data when available, references, and relevant links. The results page also includes several additional options for further analysis. These include an option to show the gene expression correlation values for each interaction and an option to filter the results by gene expression patterns or confidence scores. Utilizing these filters helps researchers to focus on interactions that are more likely to be true pos- Page 7 of 9 (page number not for citation purposes)