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 Active Regulatory Elements) on 7 cell lines from ENCODE  
DNase Clusters  DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3)  
Txn Factr ChIP E3  Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3  Data version: ENCODE 3 Nov 2018
Txn Factor ChIP  Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs  Data version: ENCODE Mar 2012 Freeze
Txn Fac ChIP V2  Transcription Factor ChIP-seq from ENCODE (V2)  Data version: ENCODE Jan 2011 Freeze

Description

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 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.

Data Access

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 here. That 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 download file for hg19.

Credits

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 restrictions. 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 Citing ENCODE.