Description

This track displays genome-wide binding profiles of DNA-associated proteins from 2,503 individual ENCODE ChIP-seq experiments, which form the experimental basis for the TF rPeaks track. These proteins include transcription factors (TFs), RNA polymerase, and chromatin-associated proteins involved in transcriptional regulation. Sequence-specific TFs bind directly to DNA motifs via DNA-binding domains, while others interact indirectly through protein-protein interactions. ChIP-seq (chromatin immunoprecipitation followed by sequencing) enables genome-wide mapping of protein-DNA interactions. Each ChIP-seq experiment is shown as two subtracks:

• Signal - a bigWig track of the experiment's signal
• Peak - a bigBed track of the experiment's peaks, colored in grayscale by ChIP-seq signal (darker = higher signal, score 0 to 1,000):

  Color	Score
  	1000 (highest signal)
  	750
  	500
  	250
  	1 (lowest signal)

Peaks often correspond to protein binding sites in specific biosamples. Additional ChIP-seq datasets can be explored through the ENCODE portal.

Display Conventions and Configuration

Click a specific protein target and organ/tissue combination to view available datasets. Subtracks can be further filtered by TF, Organ, Biosample Type, Life Stage, and Data Type (Signal or Peak).

Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ.

Data Access

The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored in bigBed files that can be downloaded from our download server. The data may also be explored interactively using our REST API. The original data files are also available from the ENCODE portal. Clicking any accession in the track's configuration table links directly to the corresponding file details page on the ENCODE portal.

These files may also be locally explored 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 features confined to a given range, e.g.,

bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/12/04/ddd64b54-7aad-4a2d-9270-ce677581b64b/ENCFF492SKF.bigBed stdout

Credits

Data were generated by the ENCODE Consortium through the following production labs: Drs. Bradley Bernstein (Broad), John Stamatoyannopoulos (UW), Kevin Struhl (HMS), Kevin White (UChicago), Michael Snyder (Stanford), Peggy Farnham (USC), Richard Myers (HAIB), Sherman Weissman (Yale), Tim Reddy (Duke), Vishwanath Iyer (UTA), and Xiang-Dong Fu (UCSD).

The data were further processed for visualization through a collaborative effort between the Weng lab and the Moore lab at UMass Chan Medical School (funded by NIH grant HG012343). Integration and visualization were developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center.

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