Description

These tracks contain information relevant to the regulation of transcription from the ENCODE Project.

• The TF rPeak Clusters track shows genomic regions bound by DNA-associated proteins involved in transcriptional regulation from ENCODE 4.
• 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.
• 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 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. 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 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.

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 the 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/hg38/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 hg38.

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.