VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Kosicki, Michael; Baltoumas, Fotis&nbsp;A; Kelman, Guy; Boverhof, Joshua; Ong, Yeongshnn; Cook, Laura&nbsp;E; Dickel, Diane&nbsp;E; Pavlopoulos, Georgios&nbsp;A; Pennacchio, Len&nbsp;A; Visel, Axel

doi:10.1093/nar/gkae940

Title: VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Journal Article · 29 October 2024 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkae940 · OSTI ID:2475236

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Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Biomedical Sciences Research Center "Alexander Fleming", Vari (Greece)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of California, Merced, CA (United States)

Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2475236

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 53; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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