Halfon Marc S, Gallo Steven M, Bergman Casey M
Department of Biochemistry, Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY 14214, USA.
Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. doi: 10.1093/nar/gkm876. Epub 2007 Nov 26.
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.
对控制基因表达的顺式调控元件进行识别和研究是生物学研究的重要领域，但用于促进后生动物物种顺式调控大规模生物信息学研究的资源却很少。黑腹果蝇具有注释良好的基因组、用于比较基因组学的出色资源以及转录调控实验研究的悠久历史，是调控生物信息学的理想系统。我们将两个现有的果蝇资源，即顺式调控模块的REDfly数据库和转录因子结合位点（TFBS）的FlyReg数据库，合并为一个单一的综合数据库，其中包含经实验验证的顺式调控模块及其组成结合位点的广泛注释。通过将TFBS数据整合到REDfly中实现了增强的功能，再加上对REDfly基础设施的进一步改进，我们构建了一个果蝇顺式调控数据的一站式门户，它将成为转录调控计算研究和实验研究的强大资源。可通过http://redfly.ccr.buffalo.edu免费访问REDfly。
