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  1. VISTA Enhancer Browser (View Publication)
    Full Name of the Resource : Enhancer elements in the human genome
    Resource Category : Databases -> Nucleotide Sequence Databases -> Coding and Coding DNA: Genes, Motifs and Regulatory Sites

    Brief 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.
    Subject Area : Human Genome;


    Institute/s :
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA
    Address of Institute/s :
    Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Country : United States

    Associated Institutes :

    • Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory Berkeley, CA 94720 USA
    • U.S. Department of Energy Joint Genome Institute, Walnut Creek CA 94598 USA

    Associated Country : USA


    Authors/Contributors : Axel Visel; Simon Minovitsky; Inna Dubchak; Len A. Pennacchio
    Contact Email : LAPennacchio@lbl.gov
    Year : 2006
    Language : English

    Keywords : Animals; Computational Biology; Databases, Nucleic Acid; Embryo, Mammalian metabolism; Enhancer Elements, Genetic; Gene Expression; Genome, Human; Genomics; Humans; Internet; Mice; User-Computer Interface