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. +
+ +Items appearing in blue (positive) indicate that a +reproducible pattern was observed in the in vivo enhancer assay under at least one of the +tested conditions. Items appearing in gray (negative) indicate +that NO reproducible pattern was observed in the in vivo enhancer assay under any of the tested +conditions. This does not exclude the possibility that this region is a reproducible enhancer active +under different conditions, for example at an earlier or later timepoint in development.
+ +Excerpted from the Vista Enhancer Mouse Enhancer Screen Handbook and Methods page at the Lawrence Berkeley +National Laboratory (LBNL) website: +
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 +vista-data bed files for +hg38 and mm10 into bigBed format using the bedToBigBed utility. The data for mm39 was lifted over +from mm10. The data for hg19 was lifted over from hg38.
+ ++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.
+ +Thanks to the Lawrence Berkeley National Laboratory for providing this data.
+ + ++Kosicki M, Baltoumas FA, Kelman G, Boverhof J, Ong Y, Cook LE, Dickel DE, Pavlopoulos GA, Pennacchio +LA, Visel A. + +VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers. +Nucleic Acids Res. 2025 Jan 6;53(D1):D324-D330. +PMID: 39470740; PMC: PMC11701537 +
++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 +