VISTA Enhancer Browser--A Database of Tissue-Specific HumanEnhancers

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Despite the known existence of distant-acting cis-regulatoryelements in the human genome, only a small fraction of these elements hasbeen identified and experimentally characterized in vivo. This paucity ofenhancer collections with defined activities has thus hinderedcomputational approaches for the genome-wide prediction of enhancers andtheir functions. To fill this void, we utilize comparative genomeanalysis to identify candidate enhancer elements in the human genomecoupled with the experimental determination of their in vivo enhanceractivity in transgenic mice (1). These data are available through theVISTA Enhancer Browser (http://enhancer.lbl.gov). This growing databasecurrently contains over 250 experimentally tested DNA fragments, of whichmore than 100 have been validated ... continued below

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Visel, Axel; Minovitsky, Simon; Dubchak, Inna & Pennacchio, Len A. August 1, 2006.

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Description

Despite the known existence of distant-acting cis-regulatoryelements in the human genome, only a small fraction of these elements hasbeen identified and experimentally characterized in vivo. This paucity ofenhancer collections with defined activities has thus hinderedcomputational approaches for the genome-wide prediction of enhancers andtheir functions. To fill this void, we utilize comparative genomeanalysis to identify candidate enhancer elements in the human genomecoupled with the experimental determination of their in vivo enhanceractivity in transgenic mice (1). These data are available through theVISTA Enhancer Browser (http://enhancer.lbl.gov). This growing databasecurrently contains over 250 experimentally tested DNA fragments, of whichmore than 100 have been validated as tissue-specific enhancers. For eachpositive enhancer, we provide digital images of whole-mount embryostaining at embryonic day 11.5 and an anatomical description of thereporter gene expression pattern. Users can retrieve elements near singlegenes of interest, search for enhancers that target reporter geneexpression to a particular tissue, or download entire collections ofenhancers with a defined tissue specificity or conservation depth. Theseexperimentally validated training sets are expected to provide a basisfor a wide range of downstream computational and functional studies ofenhancer function.

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  • Journal Name: Nucleic Acids Research; Journal Volume: 35; Journal Issue: SI; Related Information: Journal Publication Date: 01/2007

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  • Report No.: LBNL--61531
  • Grant Number: DE-AC02-05CH11231
  • Grant Number: NIHHL066681
  • Office of Scientific & Technical Information Report Number: 918925
  • Archival Resource Key: ark:/67531/metadc890009

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  • August 1, 2006

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  • Sept. 22, 2016, 2:13 a.m.

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  • Sept. 29, 2016, 7:21 p.m.

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Visel, Axel; Minovitsky, Simon; Dubchak, Inna & Pennacchio, Len A. VISTA Enhancer Browser--A Database of Tissue-Specific HumanEnhancers, article, August 1, 2006; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc890009/: accessed August 17, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.