Schema for ENCODE cCREs - ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types
  Database: mm10    Primary Table: encodeCcreCombined Data last updated: 2020-05-21
Big Bed File: /gbdb/mm10/encode3/ccre/encodeCcreCombined.bb
Item Count: 339,815
Format description: Cell-type agnostic cCRE from ENCODE. BED 9+6.
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart130342451Start position of feature on chromosome
chromEnd130342787End position of feature on chromosome
nameEM10E0449623ENCODE accession
score2240-1000, based on Z score
strand.n/a
thickStart130342451Start position
thickEnd130342787End position
reserved255,205,0RGB Color
ccredELS,CTCF-boundENCODE classification
encodeLabeldELSENCODE label
zScore2.246164729Max DNase Z-score
ucscLabelenhDUCSC label
accessionLabelE0449623Accession (abbreviated)
descriptionEM10E0449623 distal enhancer-like signatureDescription for browser hover

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedccreencodeLabelzScoreucscLabelaccessionLabeldescription
chr1130342451130342787EM10E0449623224.130342451130342787255,205,0dELS,CTCF-bounddELS2.246164729enhDE0449623EM10E0449623 distal enhancer-like signature
chr1130350270130350616EM10E0449624257.1303502701303506160,176,240CTCF-only,CTCF-boundCTCF-only2.57830541715CTCFE0449624EM10E0449624 CTCF-only
chr1130372197130372486EM10E0449625306.130372197130372486255,205,0dELS,CTCF-bounddELS3.06540329018enhDE0449625EM10E0449625 distal enhancer-like signature
chr1130373801130374060EM10E0449626297.130373801130374060255,205,0dELS,CTCF-bounddELS2.9793303545enhDE0449626EM10E0449626 distal enhancer-like signature
chr1130374215130374533EM10E0449627317.130374215130374533255,205,0dELSdELS3.17955769015enhDE0449627EM10E0449627 distal enhancer-like signature
chr1130387258130387603EM10E0449628249.130387258130387603255,205,0dELSdELS2.49650306937enhDE0449628EM10E0449628 distal enhancer-like signature
chr1130397155130397504EM10E0449629275.1303971551303975040,176,240CTCF-only,CTCF-boundCTCF-only2.7550606232CTCFE0449629EM10E0449629 CTCF-only
chr1130462183130462370EM10E0449632352.130462183130462370255,167,0pELS,CTCF-boundpELS3.52358472703enhPE0449632EM10E0449632 proximal enhancer-like signature
chr1130462440130462783EM10E0449633487.130462440130462783255,0,0PLS,CTCF-boundPLS4.8784600833promE0449633EM10E0449633 promoter-like signature
chr1130462884130463157EM10E0449634332.130462884130463157255,167,0pELS,CTCF-boundpELS3.3219608252enhPE0449634EM10E0449634 proximal enhancer-like signature

ENCODE cCREs (encodeCcreCombined) Track Description
 

Description

This track displays the ENCODE Registry of candidate cis-Regulatory Elements (cCREs) in the mouse genome, a total of 339,815 elements identified and classified by the ENCODE Data Analysis Center according to biochemical signatures. cCREs are the subset of representative DNase hypersensitive sites across ENCODE samples that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. The Registry of cCREs is one of the core components of the integrative level of the ENCODE Encyclopedia of DNA Elements.

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. The cCREs identified in the human genome are available in a companion track, here.

Display Conventions and Configuration

CCREs are colored and labeled according to classification by regulatory signature:

Color UCSC label ENCODE classification ENCODE label
red prom promoter-like signature PLS
orange enhP proximal enhancer-like signature pELS
yellow enhD distal enhancer-like signature dELS
pink K4m3 DNase-H3K4me3 DNase-H3K4me3
blue CTCF CTCF-only CTCF-only

The DNase-H3K4me3 elements are those with promoter-like biochemical signature that are not within 200bp of an annotated TSS.

Methods

All individual DNase hypsersensitive sites (DHSs) identified from 176 DNase-seq profiles in mouse (a total of 26 million) were iteratively clustered and filtered for the highest signal across all experiments, producing 1.2 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 339,815 in mouse).

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.

The GENCODE VM18 (Ensembl 93) basic gene annotation set was used in this analysis. For further detail about the identification and classification of ENCODE cCREs see the About page of the SCREEN web tool.

Data Access

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/mm10/encode3/ccre/encodeCcreCombined.bb -chrom=chr21 -start=0 -end=100000000 stdout

Release Notes

This annotation is based on ENCODE data released on or before September 14, 2018.

Credits

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.

References

ENCODE Project Consortium. Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. In press.

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