REDfly: The Regulatory Element Database for Drosophila. Marc S. Halfon^1,2,3,4, Jeffrey T. Palmer^2,5, Michael Simich^1,2, Benjamin Des Soye^1,2, Steven M. Gallo^2,5. 1) Department of Biochemistry, SUNY at Buffalo, Buffalo, NY; 2) NYS Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY; 3) Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY; 4) Molecular and Cellular Biology Department, Roswell Park Cancer Institute, Buffalo, NY; 5) Center for Computational Research, SUNY at Buffalo, Buffalo, NY.

   The REDfly database is a highly-curated portal for Drosophila cis-regulatory data containing records for empirically validated cis-regulatory modules (CRMs, enhancers) and transcription factor binding sites (TFBSs) curated from the published literature. REDfly includes all sequences reported as functionally tested in a transgenic reporter gene assay regardless of whether they showed regulatory activity or have activity redundant with other, shorter regulatory sequences. Graphical views show the position of each CRM within its genomic locus, and the location of each CRM with respect to its associated gene is provided. Curation of TFBSs includes sites identified by electrophoretic mobility shift assay (EMSA, gel shift), DNAase I footprinting, and high-throughput yeast one-hybrid assays. REDfly currently covers more than 650 publications and contains more than 5450 records of reporter constructs regulating over 500 genes, including over 1800 minimal CRMs, and over 2000 TFBSs. Extensive abilities exist for database searching and results filtering. In the coming year we hope to include the ability to search based on developmental stage as well as improved, expanded download capabilities. REDfly provides a comprehensive source of Drosophila cis-regulatory data and is a powerful platform to facilitate high-throughput experimental and computational studies of gene regulation. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.