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20 August 2010 -
New ENCODE Integrated Regulation Super-track Released
We are pleased to announce the release of the ENCODE Integrated
Regulation super-track, a collection of regulatory tracks containing
state-of-the-art information about the mechanisms that turn genes on and
off at the transcription level. Individual tracks within the set show
enrichment of histone modifications suggestive of enhancer and promoter
activity, DNAse clusters indicating open chromatin, regions of
transcription factor binding, and transcription levels. When viewed in
combination, the complementary nature of the data within these tracks
has the potential to greatly facilitate our understanding of regulatory
DNA.
The data comprising these tracks were generated from hundreds of
experiments on multiple cell lines conducted by labs participating in
the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to
the UCSC ENCODE Data Coordination Center for display on the Genome
Browser.
Faced with the problem of how to display such a large amount of data
in a manner facilitating analysis, UCSC has developed new visualization
methods that cluster and overlay the data, and then display the
resulting tracks on a single screen. Each of the cell lines in a track
is associated with a particular color. Light, saturated colors are used
to produce the best transparent overlay.
The data in the ENCODE Regulation super-track, as with all data from the
production phase of the ENCODE project, have genome-wide coverage. In
general, Genome Browser tracks that show ENCODE-generated data can be
identified by the double-helix icon preceding the name in the track
list. Currently, the ENCODE Regulation data are available only on the
March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human
genome.
For a detailed description of the datasets contained in this super-track
and a discussion of how the tracks can be used synergistically to
examine regions of regulatory functionality within the genome, see the
track description page.
18 August 2010 -
Cat Genome Browser Available:
We have released a Genome Browser for the latest assembly of Cat (Felis catus).
Read more.
23 July 2010 - BigBed/BigWig Paper Published:
We are pleased to announce that we have published a paper on
the BigBed and BigWig format.
Read more.
Kent WJ et al. BigWig and BigBed: enabling browsing of
large distributed data sets. Bioinformatics.
2010 July 17. Published online in advance of print.
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