VISTA Enhancers Track Settings
 
VISTA Enhancers   (All Regulation tracks)

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Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2023-09-27 13:17:44

Description

This track shows potential enhancers whose activity was experimentally validated in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. More information can be found on the VISTA Enhancer Browser page.

Display Conventions and Configuration

Items appearing in red (positive) indicate that a reproducible pattern was observed in the in vivo enhancer assay. Items appearing in blue (negative) indicate that NO reproducible pattern was observed in the in vivo enhancer assay. Note that this annotation refers only to the single developmental timepoint that was tested in this screen (e11.5) and does not exclude the possibility that this region is a reproducible enhancer active at earlier or later timepoints in development.

Methods

Excerpted from the Vista Enhancer Mouse Enhancer Screen Handbook and Methods page at the Lawrence Berkeley National Laboratory (LBNL) website:

Enhancer Candidate Identification

Most enhancer candidate sequences are identified by extreme evolutionary sequence conservation or by ChIP-seq. Detailed information related to enhancer identification by extreme evolutionary conservation can be found in the following publications:

Detailed information related to enhancer identification by ChIP-seq can be found in the following publications:

See the Transgenic Mouse Assay section for experimental procedures that were used to perform the transgenic assays: Mouse Enhancer Screen Handbook and Methods

UCSC converted the Experimental Data for hg19 and mm9 into bigBed format using the bedToBigBed utility. The data for hg38 was lifted over from hg19. The data for mm10 and mm39 were lifted over from mm9.

Data Access

VISTA Enhancers data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large.

Credits

Thanks to the Lawrence Berkeley National Laboratory for providing this data

References

Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92. PMID: 17130149; PMC: PMC1716724