VISTA Enhancer Browser—a database of tissue-specific human enhancers

By Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio. Nucleic Acids Res., 2006

1,107 citations recorded by the source corpus.

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 (). 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4dc53f370cdbec8d80ccfb8669a4edd655e9b58c

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Citations in the corpus

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “To reflect such distance dependency, and following previously reported convention of focusing on immediate adjacency (15), we added a distance-based measure to the gene–enhancer pairing definitions.”
Annotation of functional variation in personal genomes using RegulomeDB (2012, background): “Recently, Ward and Kellis (2012) published the HaploReg database which aims to provide a similar annotation by providing an intersect of SNVs with chromatin state (Ernst and Kellis 2010).”
Ensembl 2013 (2012, methodology): “The Ensembl Regulation database and web views continue to provide various other data resources including the following: mapping of probe sets for all the common microarray platforms, DNA methylation from various projects including ENCODE, high profile externally curated data sets such as cisRED moti”
Facilitators and Impediments of the Pluripotency Reprogramming Factors’ Initial Engagement with the Genome (2012, positive): “The functionality of early distal binding sites was underscored by the marked binding of O, S, K, and M at 48 hr to validated enhancers (Visel et al., 2007), compared to flanking regions of similar size (Figure S4B).”
Transcriptional enhancers: from properties to genome-wide predictions (2014, background): “Many promoter and enhancer candidates have so far been tested in transgenic D. melanogaster 43,121 , C. elegans 122 and mouse embryos 123 .”
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “Some of the most highly-conserved elements in vertebrates, termed Ultra-Conserved Elements (UCEs) have been tested in vivo, but only about half of these showed any capacity for specific cis-regulatory activities (8).”
The Ensembl Regulatory Build (2015, background): “Of the 882 validated human VISTA enhancers [32], 92.4% were recalled in our build.”
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods (2016, methodology): “In this report, validation is assessed using existing collections of reliable enhancers, including CAGE [4], and laboratory validated sets from CRE-seq [14], and transgenic mouse assays [37]), showing that the supervised approach nears 85.9% sensitivity.”