Description
This track collection displays candidate Cis-Regulatory Elements (cCREs) generated by the
ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3), with the ENCODE3 track
retained for archival purposes. The tracks include both integrated (biosample-agnostic) and
biosample-specific annotations derived from core epigenomic assays.
- ENCODE4 cCREs: This track presents the ENCODE Registry of 926,843
cCREs identified and classified using data
from all phases of the ENCODE Project (Phases 1-4). The registry integrates chromatin accessibility
and ChIP-seq signals across hundreds of biosamples. All cCREs are consolidated into a single,
cell type-agnostic annotation track displayed here.
- ENCODE4 Core Collection: This track displays biosample-specific cCREs alongside
genome-wide epigenomic signals for the ENCODE4 Core Collection, consisting of 18 biosamples
comprehensively profiled using four core assays: DNase-seq, ChIP-seq for H3K4me3 and
H3K27ac (histone modifications), and ChIP-seq for CTCF. These data support detailed
analysis of regulatory activity in individual biosamples.
- ENCODE3 cCREs: This track provides the version of the cCRE Registry generated
at the end of ENCODE3, using data available up to that phase. The methodology was
refined and the dataset greatly expanded during ENCODE4. While ENCODE3
tracks are preserved for reproducibility, ENCODE4 tracks are recommended for all
current analyses, as they also incorporate ENCODE3 data.
The Registry and Core Collection tracks both annotate the same 926,843 cCREs. The Registry
classifies each element cell type-agnostically using the maximum Z-score (max-Z) for each
mark across all biosamples. The Core Collection evaluates each element in specific cell types
using biosample-specific Z-scores.
Display Conventions, Data Access, and Credits
For information on track configuration, data description, data access, methods, and data provenance,
see the individual track description pages via their links above.
References
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T,
Davis CA, Dobin A et al.
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature. 2020 Jul;583(7818):699-710.
PMID: 32728249; PMC: PMC7410828
Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y et
al.
An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional
Regulation.
Nature. 2026 January 7.
PMID: 39763870; PMC: PMC11703161