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Nucleic Acids Research Advance Access published online on November 26, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm876
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

Marc S. Halfon1,2,4,5,*, Steven M. Gallo3,4 and Casey M. Bergman6

1Department of Biochemistry, 2Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY 14214, 3Center for Computational Research, 4New York State Center of Excellence in Bioinformatics and the Life Sciences, Buffalo NY 14203, 5Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo NY 14263, USA and 6Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK

*To whom correspondence should be addressed: Tel: +716-829-3126; Fax: +716-829-2725; Email: mshalfon{at}buffalo.edu

Correspondence may also be addressed to Casey M. Bergman. Tel: +44-161-275-1613; Fax: +44-161-275-5082; Email: casey.bergman{at}manchester.ac.uk

Received August 13, 2007. Revised September 12, 2007. Accepted October 1, 2007.

The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to facilitate large-scale bioinformatics studies of cis-regulation in metazoan species. Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics. We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites. With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.


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