Schema for Vista Enhancers - Vista HMR-Conserved Non-coding Human Enhancers from LBNL
  Database: hg19    Primary Table: vistaEnhancers    Row Count: 1,339   Data last updated: 2010-12-09
Format description: Browser extensible data
fieldexampleSQL type info description
bin 609smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3190581int(10) unsigned range Start position in chromosome
chromEnd 3191428int(10) unsigned range End position in chromosome
name element_705varchar(255) values Name of item
score 900int(10) unsigned range Optional score, nominal range 0-1000

Sample Rows
 
binchromchromStartchromEndnamescore
609chr131905813191428element_705900
647chr181304398131887element_1833900
665chr11059312310594209element_677200
666chr11073207010733118element_289900
667chr11075766410758631element_361200
667chr11078123910781744element_389900
667chr11085157010852173element_408900
668chr11092520210925728element_417200
668chr11096512910966144element_241900
791chr12704962027050905element_569900

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Vista Enhancers (vistaEnhancers) Track Description
 

Description and Methods

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

The VISTA Enhancer Browser identifies distant-acting transcriptional enhancers in the human genome by coupling the identification of evolutionary conserved non-coding sequences with a moderate throughput mouse transgenesis enhancer assay.

The "Experimental Dataset" of conserved non-coding human sequences has been tested for enhancer activity in transgenic mice. As of October 2006, approximately 300 elements were found in this portion of the database, and this number is expected to grow steadily. These sequences are based on UCSC human assembly hg17 (May 2004).

Non-coding elements identified as conserved in human, mouse, and rat are lifted with primers, and the PCR fragment is cloned into a reporter vector that has a minimal promoter fused to LacZ. This is then injected into a fertilized mouse egg and the 11.5 day embryo is assayed for activity with lacZ stain. Whole-embryo in situ pictures are available on the LBNL website..

To be defined as a positive enhancer, an element has to show reproducible expression in the same structure in at least three independent transgenic embryos. An element is defined as negative if at least five transgenic embryos have been obtained, but no reproducible expression was observed in any structure in at least three different embryos.

Users should keep in mind that the assay captures only a single embryonic timepoint. A negative result reported in the experimental dataset does not necessarily imply that this conserved element is not a transcriptional enhancer, because it might be active at earlier or later timepoints in development.

Display Conventions and Configuration

Elements that tested positive are assigned a score of 900 and display in black in the annotation track. Those that tested negative are given the score 200 and appear as light grey.

Credits

Thanks to Len Pennacchio at Lawrence Berkeley National Laboratory for providing the enhancer track.

References

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23;444(7118):499-502. PMID: 17086198