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Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. Epub 2007 Nov 26.

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

Author information

1
Department of Biochemistry, Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY 14214, USA. mshalfon@buffalo.edu

Abstract

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.

PMID:
18039705
PMCID:
PMC2238825
DOI:
10.1093/nar/gkm876
[Indexed for MEDLINE]
Free PMC Article

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