-This track displays the ENCODE Registry of candidate cis-Regulatory Elements (cCREs) -in the genome, identified and classified by the ENCODE Data Analysis Center according to -regulatory effect. -CCREs are the subset of DNase hypersensitivity sites clustered across all samples -that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. -The cCRE dataset is the core of the integrative level of epigenomic and transcriptomic -annotations produced by ENCODE. -The registry currently comprises a total of 926,535 elements in the human genome and 339,815 -in the mouse genome (less comprehensively assayed). -
-Additional exploration of the cCRE's and underlying raw ENCODE data is provided by the - -SCREEN -(Search Candidate cis-Regulatory Elements) web tool, -designed specifically for the registry, and accessible by linkouts from the track details page. - - - --CCREs are colored and labeled according to classification by regulatory signature: -
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| Color | -- | Label | -Classification | -- |
|---|---|---|---|---|
| red | -prom | -promoter-like | -PLS | |
| orange | -enhP | -proximal enhancer-like | -pELS | |
| yellow | -enhD | -distal enhancer-like | -dELS | |
| blue | -CTCF | -CTCF-only | -CTCF-only | |
| pink | -K4m3 | -DNase-H3K4me3 | -DNase-H3K4me3 |
-The DNase-H3K4me3 elements are those with promoter-like biochemical signature that -are not within 200bp of an annotated TSS. -
- --All individual DNase hypsersensitivity sites (DHSs) identified from DNAse-seq experiments -(in human, a total of 93 million sites from 706 experiments) were iteratively clustered -and filtered for highest signal across all experiments, producing -representative DHSs (rDHSs), with a total of 2.2 million such sites in human. -The highest signal elements from this set that were also supported by high H3K4me3, H3K27ac -and/or CTCF ChIP-seq signals were designated cCRE's (a total of 926,535 in human). -
--Classification of cCRE's was performed based on the following criteria: -
-
-1. cCREs with promoter-like signatures (cCRE-PLS) fall within 200 bp of -an annotated GENCODE TSS and have high DNase and H3K4me3 signals. -
--2. cCREs with enhancer-like signatures (cCRE-ELS) have high DNase and H3K27ac -with low H3K4me3 max-Z score if they are within 200 bp of an annotated TSS. -The subset of cCREs-ELS within 2 kb of a TSS is denoted proximal (cCRE-pELS), -while the remaining subset is denoted distal (cCRE-dELS). -
- --3. DNase-H3K4me3 cCREs have high H3K4me3 max-Z scores but low H3K27ac max-Z scores -and do not fall within 200 bp of a TSS. -
- --4. CTCF-only cCREs have high DNase and CTCF and low H3K4me3 and H3K27ac. -
- -
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--For further detail about the identification and classification of ENCODE cCREs see -the About page of the -SCREEN web tool. -
- --The ENCODE accession numbers of the constituent datasets at the -ENCODE Portal -are available from the cCRE details page. -
--The data in this track can be interactively explored with the -Table Browser or the -Data Integrator. -The data can be accessed from scripts through our -API, the track name is "encodeCcreCombined". - -
-For automated download and analysis, this annotation is stored in a bigBed file that -can be downloaded from -our download server. -The file for this track is called encodeCcreCombined.bb. -Individual regions or the whole genome annotation can be obtained using our tool -bigBedToBed which can be compiled from the source code or downloaded as a precompiled -binary for your system. -Instructions for downloading source code and binaries can be found -here. -The tool can also be used to obtain only features within a given range, e.g. -bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/encodeCcreCombined.bb -chrom=chr21 -start=0 -end=100000000 stdout
- - --This dataset was produced by the ENCODE Data Analysis Center ( -Zlab - at UMass Medical Center). -Thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI for providing -this data. -Thanks also to the ENCODE Consortium, the ENCODE production laboratories, -and the ENCODE Data Coordination Center for generating and processing the datasets used here. -
- --ENCODE Project Consortium.. - -An integrated encyclopedia of DNA elements in the human genome. -Nature. 2012 Sep 6;489(7414):57-74. -PMID: 22955616; PMC: PMC3439153 -
- -ENCODE Project Consortium.. - -A user's guide to the encyclopedia of DNA elements (ENCODE). -PLoS Biol. 2011 Apr;9(4):e1001046. -PMID: 21526222; PMC: PMC3079585 - -