This track displays genome-wide binding profiles of DNA-associated proteins from 334 individual ENCODE ChIP-seq experiments. 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 subtrack represents an individual ChIP-seq experiment, showing signal peaks that often correspond to protein binding sites in specific biosamples. Additional ChIP-seq datasets can be explored through the ENCODE portal.
This composite contains both signal (bigWig) and peak (bigBed) data for each experiment, selectable via the "Data Type" facet in the track settings.
Click a specific protein target and organ/tissue combination to view available datasets. Subtracks can be further filtered by the type and life stage of the biosample. Each peak is displayed as a bigBed item, shaded in grayscale with intensity reflecting the ChIP-seq signal strength.
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 bigWig (signal) and bigBed (peak) 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.
Signal files may be locally explored using bigWigToWig, e.g.,
bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/11/24/559f88bd-29ea-4694-9cdf-3eddf3d87e0e/ENCFF265VZJ.bigBed stdout
Peak files may be explored using bigBedToBed, e.g.,
bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/11/24/559f88bd-29ea-4694-9cdf-3eddf3d87e0e/ENCFF265VZJ.bigBed stdout
Instructions for downloading these tools can be found
here.
Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Barbara Wold (Caltech), Bing Ren (UCSD), Christine Disteche (UW), Michael Snyder (Stanford), Richard Myers (HAIB), and Ross Hardison (PennState).
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.
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