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 Overlayed
H3K4Me1 and Overlayed H3K27Ac tracks show where modification of histone proteins
is suggestive of enhancer and, to a lesser extent, other regulatory 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 Overlay 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
tracks show 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
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 raw data for ENCODE 3 Regulation tracks can be accessed from
Table Browser or combined with other data-sets through
Data Integrator. For automated analysis and downloads, the track data files can be downloaded
from our downloads server or queried
using the JSON API or
Public SQL. Individual regions or the whole genome
annotation can be accessed as text using our utility bigBedToBed. Instructions for
downloading the utility can be found
utility can also be used to obtain features within a given range, e.g.
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/wgEncodeRegDnase/wgEncodeRegDnaseUwA549Hotspot.broadPeak.bb -chrom=chr21 -start=0 -end=100000000 stdout
For sorting transcription factor binding sites by cell type, we recommend you use the following
file for hg19.
Specific labs and contributors for these datasets are listed in the Credits section
of the individual tracks in this super-track.
The integrative view presented here was developed by Jim Kent at UCSC.
Data Use Policy
Users may freely download, analyze and publish results based on any ENCODE data without
Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional.
Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE
production laboratory(s) that generated the datasets used, as described in