Vista Enhancers Track Settings
 
Vista HMR-Conserved Non-coding Human Enhancers from LBNL   (All Regulation tracks)

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Show only items with score at or above:   (range: 0 to 1000)

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Data last updated: 2010-12-09

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.