Database Commons a catalog of biological databases

Database Commons - VEB

VEB

Citations: 340

z-index 10.20

Short name VEB
Full name VISTA Enhancer Browser
Description The VISTA Enhancer Browser is a central resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice.
URL http://enhancer.lbl.gov/
Year founded 2007
Last update & version 2006-11-27    v1.0
Availability Free to all users
University/Institution hosted Lawrence Berkeley National Laboratory
Address 1 Cyclotron Rd, Berkeley, CA 94720
City Berkeley
Province/State CA
Country/Region United States
Contact name Len A. Pennacchio
Contact email LAPennacchio@lbl.gov
Data type(s)
Major organism(s)
Keyword(s)
  • cis-regulatory element
Publication(s)
  • VISTA Enhancer Browser--a database of tissue-specific human enhancers. [PMID: 17130149]

    Axel Visel, Simon Minovitsky, Inna Dubchak, Len A Pennacchio
    Nucleic acids research 2007:35(Database issue)
    340 Citations (Google Scholar as of 2016-04-30)

    Abstract: 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 [L. A. Pennacchio et al. (2006) Nature, in press]. 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.

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Tags

DNA
Homo sapiens
cis-regulatory element

Record metadata

  • Created on: 2015-08-10
  • Curated by:
    • Hongyan Yin [2016-03-31]
    • Mengwei Li [2016-02-15]
    • Hongyan Yin [2015-12-06]
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