+This track displays the ENCODE Registry of candidate cis-Regulatory Elements (cCREs) in +the human genome, a total of 926,535 elements identified and classified by the +ENCODE Data Analysis Center according to regulatory effect. +cCREs are the subset of DNase hypersensitivity sites clustered across all ENCODE 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. +
+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, accessible by linkouts from the track details page. + + + ++CCREs are colored according to classification by regulatory signature: +
+
| Color | ++ | Group | ++ |
|---|---|---|---|
| red | +promoter-like | +PLS | |
| orange | +proximal enhancer-like | +pELS | |
| yellow | +distal enhancer-like | +dELS | |
| blue | +CTCF-only | +CTCF-only | |
| pink | +DNase-H3K4me3 | +DNase-H3K4me3 |
+All individual DNase hypsersensitivity sites (DHSs) identified from 706 DNAse-seq experiments +in human (a total of 93 million) were iteratively clustered and filtered +for highest signal across all experiments, producing 2.2 million representative DHSs (rDHSs). +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. +
+ +
+
++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 + +