ENCODE Regulation Super-track Settings
Integrated Regulation from ENCODE Tracks   (All Regulation tracks)

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Transcription  Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
Layered H3K4Me1  H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
Layered H3K4Me3  H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
Layered H3K27Ac  H3K27Ac Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
DNase Clusters  DNase I Hypersensitivity Peak Clusters from ENCODE (95 cell types)
DNase Signal  DNase I Hypersensitivity Signal Colored by Similarity from ENCODE
DNase HS  DNase I Hypersensitivity in 95 cell types from ENCODE


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 Layered H3K4Me1 and Layered 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 Layered H3K4Me3 track shows a histone mark associated with promoters.
  • The DNase I Hypersensitivity tracks indicate where 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.

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 hypersensitivity 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. 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 supertrack just shows a selection of the most informative data of most general interest.

Display Conventions

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. The color of the transcription and histone mark tracks match their versions from their lifted source on the hg19 assembly.

The DNase tracks, which were not lifted from hg19, are colored differently to reflect similarity of cell types. There are three DNase tracks starting with a transparent overlay DNase Signal Track to allow viewing signals from all 95 cell types in one track. The individual signals and the same coloring scheme can also be found in the DNase HS Track where processed peaks and hotspots are also called out as gray boxes with the darkness of each box reflecting the underlying signal value. Lastly, in the DNase Clusters track all observed hypersensitive regions in the different cell lines at the same location were clustered into a single box where a number to the left of the box indicates how many cell types showed a hypersensitivity region and the darkness of the grey box is proportional to the the maximum value seen from one of the underlying cell lines. Clicking on these item takes you to a details page where additional information displays, such as the list of cell types that combined to form the cluster in the DNase Clusters track.


The data in this supertrack comes from the ENCODE grants led by Bradley Bernstein (Broad Institute), Richard Myers (HudsonAlpha Institute), Michael Snyder (Stanford), Gregory Crawford (Duke) 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 supertrack. The integrative view was developed by Jim Kent at UCSC.

Data Release Policy

Primary ENCODE data produced during the 2007-2012 production phase were subject to a restriction period. However, the data here are past those restrictions and are freely available. The full data release policy for ENCODE is available here.