ENCODE Regulation DNase Clusters Track Settings

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DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3)

Track collection: Integrated Regulation from ENCODE

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.

To view the full description, click here.

All tracks in this collection (8)

Display mode:

Minimum Display score (0-1000):

(100 to 1000)

Metadata:

tableName:	wgEncodeRegDnaseClusteredV3
File Name for downloading:	wgEncodeRegDnaseClusteredV3.bed.gz

View table schema

Data last updated at UCSC: 2019-01-09

Description

This track shows DNase hypersensitive areas assayed in a large collection of cell types by the ENCODE project. Regulatory regions in general, and promoters in particular, tend to be DNase-sensitive. Additional views of this data and additional documentation on the methods used to identify hypersensitive sites are available from the Uniform DNaseI HS page. The uniform peaks in that track are the basis for the clusters shown here, which combine data from the peaks of the different cell lines.

Display Conventions and Configuration

A gray box indicates the extent of the hypersensitive region. The darkness is proportional to the maximum signal strength observed in any cell line. The number to the left of the box shows how many cell lines are hypersensitive in the region. The track can be configured to restrict the display to elements above a specified score in the range 100-1000 (where score is based on signal strength).

Methods

Stringent (FDR 1% thresholded) peaks of DNaseI hypersensitivity from uniform processing by the ENCODE Analysis Working Group (Uniform DNaseI HS) were assigned normalized scores (by UCSC regClusterMakeTableOfTables) in the range 0-1000 based on the narrowPeak signalValue and then clustered on score (by UCSC regCluster) to generate singly-linked clusters. Low-scoring clusters (score <100) were then filtered out.

Release Notes

This is the third release of this track. It differs from the previous track as it includes clusters having only 1 cell type contributing to the cluster (previously excluded). The previous track is available on the UCSC preview browser as DNase Clusters V2.

Credits

This track shows data from the University of Washington and Duke ENCODE groups, with uniform processing by the ENCODE Analysis Working Group. The clustering was performed at UCSC. For additional credits and references, see the Uniform DNaseI HS page.

Data Release Policy

While primary ENCODE data is subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results. The data in this track are freely available.