PgmNr D1526: REDfly: The Regulatory Element Database for Drosophila.

Authors:
M. S. Halfon 1,2,3 ; M. Zia 1,2 ; S. M. Gallo 1,2


Institutes
1) University at Buffalo, Buffalo, NY; 2) New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY; 3) Roswell Park Cancer Institute, Buffalo, NY.


Keyword: webtools and databases

Abstract:

The REDfly database is a curated portal for Drosophila cis-regulatory data containing records for empirically validated cis-regulatory modules (CRMs, “enhancers”) and transcription factor binding sites (TFBSs) reported in the published literature. REDfly’s goal is to include all functionally tested sequences regardless of whether they have observable 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 680 publications and contains more than 11,600 records of reporter constructs regulating over 550 genes, including over 5600 “minimal” CRMs,  as well as over 2000 TFBSs. Extensive abilities exist for database searching and results filtering. In 2015 we released REDfly v4 including updates to release 6 genome coordinates, an option to download sequences in BED format, and numerous behind-the-scenes improvements. REDfly v5.0 was released in Spring 2016 with fully updated genome annotations and anatomical descriptions. Search has been updated to optionally retrieve all annotated CRMs within a user-defined distance of a locus, not just CRMs explicitly associated with a specific gene. Additional improvements scheduled for release in 2016 include further improved search and download capabilities, addition of ChIP-derived TFBSs, predicted CRMs, integration with Galaxy, and substantial new curation. 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 and can be followed on Twitter at @REDfly_database.