ENCODE Regulation Transcription Track Settings
 
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 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)
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
Txn Factor ChIP Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs
Txn Fac ChIP V2 Transcription Factor ChIP-seq from ENCODE (V2)

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      GM12878  Transcription of GM12878 cells from ENCODE    Data format   2011-10-21 
      H1-hESC  Transcription of H1-hESC cells from ENCODE    Data format   2011-10-21 
      HeLa-S3  Transcription of HeLa-S3 cells from ENCODE    Data format   2010-10-12 
      HepG2  Transcription of HepG2 cells from ENCODE    Data format   2010-10-11 
      HSMM  Transcription of HSMM cells from ENCODE    Data format   2011-10-21 
      HUVEC  Transcription of HUVEC cells from ENCODE    Data format   2011-10-21 
      K562  Transcription of K562 cells from ENCODE    Data format   2011-10-21 
      NHEK  Transcription of NHEK cells from ENCODE    Data format   2011-10-21 
      NHLF  Transcription of NHLF cells from ENCODE    Data format   2011-10-21 
    
Assembly: Human Feb. 2009 (GRCh37/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 cell line colors are consistent across all tracks that are part of the ENCODE Regulation supertrack. 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.

Credits

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

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, above. The full data release policy for ENCODE is available here.