ENCODE4 Regulation Transcription (Layered) Track Settings

Strand-specific transcription signal measured by total RNA-seq, averaged by organ/tissue

Configure track container: Integrated Regulation from ENCODE 4

Description

This collection of tracks offers an integrated view of genomic annotations and experimental data from all phases of the ENCODE Project, with a focus on transcriptional regulation. It includes averaged and representative signals from assays that measure chromatin accessibility (DNase-seq and ATAC-seq), transcription factor (TF) binding (ChIP-seq for individual TFs), histone modifications (ChIP-seq for H3K4me3 and H3K27ac), CTCF binding, and transcription (RNA-seq).

Tracks labeled (Layered) show organ-averaged signals as a transparent overlay of multiple organs within a single track. Tracks labeled (Indiv.) show signals from individual experiments in specific biosamples.

The H3K27ac (Layered) track displays enrichment levels of a histone modification associated with active enhancers and promoters, averaged across 19 organs.
The DNase (Layered) track displays regions of chromatin that are hypersensitive to DNase I digestion, indicating open and potentially regulatory chromatin. Signal is averaged across biosamples from the same organ for 26 organs.
The ATAC (Layered) track displays regions of open chromatin identified by ATAC-seq, which uses Tn5 transposase insertion to assay accessibility. Signal is averaged across 12 organs.
The H3K4me3 (Layered) track displays enrichment levels of a histone modification associated with active or poised promoters, averaged across 20 organs.
The CTCF (Layered) track displays genomic regions bound by CTCF, a multifunctional DNA-binding protein involved in chromatin organization and gene regulation. Signal is averaged across 16 organs.
The Transcription (Layered) track displays transcription levels measured by strand-specific total RNA-seq across a large number of biosamples, shown separately for the two genomic strands.
The TF ChIP-seq (Indiv.), DNase/ATAC/Histone/CTCF (Indiv.), and RNA-seq (Indiv.) tracks display signals from individual experiments in specific biosamples.

These tracks complement one another and collectively provide a resource for interpreting regulatory DNA. Histone marks are broadly informative but have limited resolution (~200 bp) and relatively low functional specificity. DNase-seq assays offer higher resolution and scalability across many cell types, and they reliably indicate regulatory potential, though they lack detailed functional context. ATAC-seq serves a similar role to DNase-seq, with comparable resolution and limitations. Transcription factor ChIP-seq has high positional resolution and, due to the specificity of TFs, often provides more direct functional insight. However, because each TF must be assayed individually, the data are limited in biosample coverage. Despite the individual strengths and limitations of these assays, their independence from one another increases confidence when multiple assays suggest a regulatory function for the same genomic region.

For additional information, click on the hyperlinks for the individual tracks above. Additional histone marks and transcription data are available in other ENCODE tracks. This integrative supertrack presents a curated selection of the most informative and broadly relevant datasets. Further functional annotations of individual regulatory elements are available at SCREEN.

For annotations of individual regulatory elements, see the related ENCODE cCREs track.

To view the full description, click here.

All tracks in this collection (9)

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	adrenal gland +	Avg. + strand total RNA-seq level of 35 adrenal gland experiments (tissues and primary cells only)	Data format
	adrenal gland -	Avg. - strand total RNA-seq level of 35 adrenal gland experiments (tissues and primary cells only)	Data format
	blood +	Avg. + strand total RNA-seq level of 53 blood experiments (tissues and primary cells only)	Data format
	blood -	Avg. - strand total RNA-seq level of 53 blood experiments (tissues and primary cells only)	Data format
	bone marrow +	Avg. + strand total RNA-seq level of 242 bone marrow experiments (tissues and primary cells only)	Data format
	bone marrow -	Avg. - strand total RNA-seq level of 242 bone marrow experiments (tissues and primary cells only)	Data format
	brain +	Avg. + strand total RNA-seq level of 80 brain experiments (tissues and primary cells only)	Data format
	brain -	Avg. - strand total RNA-seq level of 80 brain experiments (tissues and primary cells only)	Data format
	heart +	Avg. + strand total RNA-seq level of 40 heart experiments (tissues and primary cells only)	Data format
	heart -	Avg. - strand total RNA-seq level of 40 heart experiments (tissues and primary cells only)	Data format
	liver +	Avg. + strand total RNA-seq level of 4 liver experiments (tissues and primary cells only)	Data format
	liver -	Avg. - strand total RNA-seq level of 4 liver experiments (tissues and primary cells only)	Data format
	muscle +	Avg. + strand total RNA-seq level of 35 muscle experiments (tissues and primary cells only)	Data format
	muscle -	Avg. - strand total RNA-seq level of 35 muscle experiments (tissues and primary cells only)	Data format
	blood + (all biosamples)	Avg. + strand total RNA-seq level of 71 blood experiments (all biosamples)	Data format
	blood - (all biosamples)	Avg. - strand total RNA-seq level of 71 blood experiments (all biosamples)	Data format
	embryo + (all biosamples)	Avg. + strand total RNA-seq level of 12 embryo experiments (all biosamples)	Data format
	embryo - (all biosamples)	Avg. - strand total RNA-seq level of 12 embryo experiments (all biosamples)	Data format
	spleen + (all biosamples)	Avg. + strand total RNA-seq level of 4 spleen experiments (all biosamples)	Data format
	spleen - (all biosamples)	Avg. - strand total RNA-seq level of 4 spleen experiments (all biosamples)	Data format

Assembly: Mouse Dec. 2011 (GRCm38/mm10)

Description

For each organ, this track provides up to two subtracks averaging total RNA-seq signal per strand:

Tissue and Primary Cell averages only the tissue and primary cell experiments.
All Biosamples averages every experiment for that organ, including the tissue/primary cell ones plus any from cell lines, in vitro differentiated cells, or organoids.

Each subtrack provides separate signal tracks for the plus and minus genomic strands. Whether one or two pairs of strand subtracks appear for an organ depends on which kinds of biosamples have been assayed:

Tissue/primary cell only. There are no cell line, in vitro differentiated cell, or organoid experiments to include, so the two averages would be computed from the same data and produce identical numbers. Only the Tissue and Primary Cell pair (plus and minus strand) is shown.
Cell line, in vitro differentiated cell, or organoid experiments only. There are no tissue or primary cell experiments to average, so only the All Biosamples pair is shown. In this case it represents those experiments.
Both kinds of biosamples available. The two averages give different numbers because one covers only the tissue and primary cell experiments while the other includes everything together. Both pairs of subtracks are shown.

Available Organs and Tissues

Organ/Tissue	Tissue and Primary Cell Subtrack	All Biosamples Subtrack
adrenal gland	✓	–
blood	✓	✓
bone marrow	✓	–
brain	✓	–
embryo	–	✓
heart	✓	–
liver	✓	–
muscle	✓	–
spleen	–	✓

Display Conventions and Configuration

By default, this track uses a transparent overlay to visualize data from multiple organs or tissues within the same vertical space. For each organ or tissue, signals from all associated experiments were averaged to generate the displayed track. Each organ or tissue is assigned a distinct color following the ENCODE color mapping convention, selected to be light and saturated to maintain clarity when overlaid. Initially, each layered track displays an overlay of five representative organs: blood, brain, kidney, liver, and muscle. Clicking on the track opens a details page where you can view and select organs or tissues. Subtracks can be further filtered by strandedness (+ strand or - strand) and life stage of the biosample.

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 bigWig 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.

These files may also be locally explored using our tool bigWigToWig, 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 data confined to a given range, e.g.,

bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://hgdownload.soe.ucsc.edu/gbdb/mm10/encode4/regulation/organAve/adrenalGlandPlus.bw stdout

Credits

Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Alexander Hoffmann (UCLA), Barbara Wold (Caltech), Manuel Garber (UMass), Michael Snyder (Stanford), Ross Hardison (PennState), and Thomas Gingeras (CSHL). 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