Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryos. By clicking on specific locations in an embryo associated with a specific data source, stage range, and anatomical orientation, researchers can rapidly find co-expressed genes and relevant peer-reviewed publications.

The FlyExpress digital library contains over 100,000 embryo images collected from >4500 genes and more than 2600 peer-reviewed publications. Users can browse images, search for co-expressed genes and genomic elements, discover motifs, and create publication quality genome-wide expression maps for a collection of genes. In addition, FlyExpress also offers downloadable standalone desktop software for image storage, analysis, and retrieval.