These tracks contain information relevant to the regulation of transcription from the
ENCODE project. The Transcription track shows transcription
levels assayed by sequencing of polyadenylated RNA from a variety of cell types. The Enhancer
H3K4Me1 and Enhancer H3K27Ac tracks show where modification of histone proteins
is suggestive of enhancer and, to a lesser extent, promoter activity. These histone
modifications, particularly H3K4Me1, are quite broad. The actual enhancers are typically just a
small portion of the area marked by these histone modifications. The Promoter H3K4Me3
track shows a histone mark associated with promoters. The DNase Clusters track shows regions
where the chromatin is hypersensitive to cutting by the DNase enzyme, which has
been assayed in a large number of cell types. Regulatory regions, in general, tend to be
DNase sensitive, and promoters are particularly DNase sensitive. The Txn Factor ChIP
track shows DNA regions where transcription factors, proteins responsible for
modulating gene transcription, bind as assayed by chromatin immunoprecipitation with antibodies
specific to the transcription factor followed by sequencing of the precipitated DNA (ChIP-seq).
These tracks complement each other and together can shed much light on regulatory DNA. The histone
marks are informative at a high level, but they have a resolution of just ~200 bases and do not
provide much in the way of functional detail. The DNase hypersensitive assay is higher in
resolution at the DNA level and can be done on a large number of cell types since it's just
a single assay. At the functional level, DNase hypersensitivity suggests that a
region is very likely to be regulatory in nature, but provides little information beyond that. The transcription
factor ChIP assay has a high resolution at the DNA level, and, due to the very specific nature
of the transcription factors, is often informative with respect to functional detail. However, since each
transcription factor must be assayed separately, the information is
only available for a limited number of transcription factors on a limited number of cell lines.
Though each assay has its strengths and weaknesses, the fact that all of these assays are
relatively independent of each other gives increased confidence when multiple tracks are
suggesting a regulatory function for a region.
For additional information please click on the hyperlinks for the individual tracks above.
Also note that additional histone marks and transcription information is available in other
ENCODE tracks. This integrative Super-track just shows a selection of the most informative data of
most general interest.
By default, the transcription and histone mark displays use a transparent overlay method of
displaying data from a number of cell lines in a single track. Each of the cell lines in this track is associated with a particular
color, and these colors are relatively light and saturated so
as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line
color conventions are used that don't match the cell line colors used in
the ENCODE Regulation tracks. The older colors were not used in the
ENCODE Regulation tracks because they were too dark for the transparent
overlay. The DNase and Transcription Factor ChIP tracks contain information on so many cell lines that a color convention
is inadequate. Instead, these tracks show gray boxes where the darkness of
the box is proportional to the maximum value seen in any cell line in that region. Clicking on
the item takes you to a details page where the values for each cell line assayed are displayed.
The data in this super-track comes from the ENCODE grants led by Bradley Bernstein (Broad Institute),
Richard Myers (HudsonAlpha Institute), Michael Snyder (Stanford) and John Stamatoyannopoulos
(University of Washington). Specific labs and contributors for these datasets are listed in
the Credits section of the individual tracks in this super-track. The integrative view was
developed by Jim Kent at UCSC.
Data Release Policy
Data users may freely use ENCODE data, but may not, without prior
consent, submit publications that use an unpublished ENCODE dataset until
nine months following the release of the dataset. This date is listed in
the Restricted Until column on the track configuration page and the download page. The full data release policy
for ENCODE is available