ENCODE Regulation Transcription Track Settings

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Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE

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 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.

To view the full description, click here.

All tracks in this collection (9)

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	GM12878	Transcription of GM12878 cells from ENCODE	Data format
	H1-hESC	Transcription of H1-hESC cells from ENCODE	Data format
	HeLa-S3	Transcription of HeLa-S3 cells from ENCODE	Data format
	HepG2	Transcription of HepG2 cells from ENCODE	Data format
	HSMM	Transcription of HSMM cells from ENCODE	Data format
	HUVEC	Transcription of HUVEC cells from ENCODE	Data format
	K562	Transcription of K562 cells from ENCODE	Data format
	NHEK	Transcription of NHEK cells from ENCODE	Data format
	NHLF	Transcription of NHLF cells from ENCODE	Data format

Assembly: Human Dec. 2013 (GRCh38/hg38)
Data coordinates converted via liftOver from: Feb. 2009 (GRCh37/hg19)

Note: lifted from hg19

Description

This track shows transcription levels for several cell types as assayed by high-throughput sequencing of polyadenylated RNA (RNA-seq). Additional views of this dataset and additional documentation on the methods used for this track are available at the ENCODE Caltech RNA-seq page. The data shown here are derived from the Raw Signal view from the paired 75-mer 200 bp insert size reads. The two replicates of the signal were pooled and normalized so that the total genome-wide signal sums to 10 billion.

Display Conventions and Configuration

By default, this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. 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 these tracks match their versions from their lifted source on the hg19 assembly. The colors are consistent with the other hg19 lifted tracks located in the ENCODE Regulation supertrack, with the exception being the DNase tracks, as they were not lifted from hg19 and are colored to reflect similarity of cell types.

Credits

This track shows data from the Wold Lab at Caltech, as part of the ENCODE Consortium.

Release Notes

This is release 2 (July 2012) of this track which includes two new subtracks for HeLa-S3 and HepG2.

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.