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

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Transcription  ENCODE Transcription Levels Assayed by RNA-seq on 6 Cell Lines  
Layered H3K4Me1  ENCODE Enhancer- and Promoter-Associated Histone Mark (H3K4Me1) on 8 Cell Lines  
Enhanced H3K27Ac  ENCODE Enhancer- and Promoter-Associated Histone Mark (H3K27Ac) on 8 Cell Lines  
Layered H3K4Me3  ENCODE Promoter-Associated Histone Mark (H3K4Me3) on 9 Cell Lines  
DNase Clusters  ENCODE Digital DNaseI Hypersensitivity Clusters  
Txn Factor ChIP  ENCODE Transcription Factor ChIP-seq  


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.

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. 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 here.