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

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

2007 | Axel Visel¹, Simon Minovitsky¹, Inna Dubchak¹,² and Len A. Pennacchio¹,²
The VISTA Enhancer Browser is a database of tissue-specific human enhancers. It provides access to experimentally validated enhancer elements identified through comparative genomics and tested in transgenic mice. The database contains over 250 experimentally tested DNA fragments, with more than 100 validated as tissue-specific enhancers. Each positive enhancer is associated with digital images of whole-mount embryo staining and anatomical descriptions of reporter gene expression patterns. Users can retrieve elements near genes of interest, search for enhancers targeting specific tissues, or download collections of enhancers with defined tissue specificity or conservation depth. The database also includes a computational dataset of over 145,000 conserved non-coding sequences, identified based on conservation between human, mouse, and rat. These elements are analyzed for conservation in other vertebrates to determine their conservation depth. The VISTA Enhancer Browser is a public resource that facilitates access to in vivo enhancer data for both experimental and computational biologists. It allows users to query datasets, including both experimentally tested and computationally predicted enhancers. The database is continuously updated with new data and is available for free without registration. The browser is hosted at the Lawrence Berkeley National Laboratory and is accessible at http://enhancer.lbl.gov. The database supports bulk downloads of sequences and provides detailed information on enhancer activity, including conservation depth and tissue specificity. The VISTA Enhancer Browser aims to improve interoperability with other resources and enhance tools for data deposition and searching by external users. It is expected to serve as a valuable resource for the study of enhancer function and regulation.The VISTA Enhancer Browser is a database of tissue-specific human enhancers. It provides access to experimentally validated enhancer elements identified through comparative genomics and tested in transgenic mice. The database contains over 250 experimentally tested DNA fragments, with more than 100 validated as tissue-specific enhancers. Each positive enhancer is associated with digital images of whole-mount embryo staining and anatomical descriptions of reporter gene expression patterns. Users can retrieve elements near genes of interest, search for enhancers targeting specific tissues, or download collections of enhancers with defined tissue specificity or conservation depth. The database also includes a computational dataset of over 145,000 conserved non-coding sequences, identified based on conservation between human, mouse, and rat. These elements are analyzed for conservation in other vertebrates to determine their conservation depth. The VISTA Enhancer Browser is a public resource that facilitates access to in vivo enhancer data for both experimental and computational biologists. It allows users to query datasets, including both experimentally tested and computationally predicted enhancers. The database is continuously updated with new data and is available for free without registration. The browser is hosted at the Lawrence Berkeley National Laboratory and is accessible at http://enhancer.lbl.gov. The database supports bulk downloads of sequences and provides detailed information on enhancer activity, including conservation depth and tissue specificity. The VISTA Enhancer Browser aims to improve interoperability with other resources and enhance tools for data deposition and searching by external users. It is expected to serve as a valuable resource for the study of enhancer function and regulation.
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[slides and audio] VISTA Enhancer Browser%E2%80%94a database of tissue-specific human enhancers