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VISTA Enhancer Browser


NAR Molecular Biology Database Collection entry number 968
Visel A.1, Minovitsky S.1, Dubchak I.1,2 and Pennacchio L.A.1,2
1Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
2U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA

Database Description

Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions. To fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice. These data are available through the VISTA Enhancer Browser (http://enhancer.lbl.gov). This growing database currently contains over 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers. For each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth. These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function.

Recent Developments

An online tutorial for VISTA databases and tools is available at http://www.openhelix.com/downloads/vista/vista_tutorialhome.shtml.

Acknowledgements

Research is conducted at the E.O. Lawrence Berkeley National Laboratory, supported by grant HL066681 (L.A.P., I.D and S.M.), Berkeley-PGA, under the Programs for Genomic Applications, funded by National Heart, Lung, & Blood Institute and by HG003988 (L.A.P.) funded by National Human Genome Research Institute, and performed under Department of Energy Contract DE-AC02-05CH11231, University of California. A.V. is supported by an American Heart Association postdoctoral fellowship.

References

1. Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M.I., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K.D., Plajzer-Frick, I., Akiyama, J., De Val, S., Afzal, V., Black, B.L., Couronne, O., Eisen, M.B., Visel, A., Rubin, E.M. (2006) In Vivo Enhancer Analysis of Human Conserved Non-Coding Sequences. Nature, (in press)
2.Visel, A., Minovitsky, S., Dubchak, I., Pennacchio, L.A. (2007) VISTA Enhancer Browser—A Database of Tissue-Specific Human Enhancers. Nucleic Acids Res. 35: in press


Go to the abstract in the NAR 2007 Database Issue.
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