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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

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     Adipose +  Avg. + strand total RNA-seq level of 9 adipose experiments (tissues and primary cells only)   Data format 
     Adipose -  Avg. - strand total RNA-seq level of 9 adipose experiments (tissues and primary cells only)   Data format 
     Adrenal gland +  Avg. + strand total RNA-seq level of 8 adrenal gland experiments (tissues and primary cells only)   Data format 
     Adrenal gland -  Avg. - strand total RNA-seq level of 8 adrenal gland experiments (tissues and primary cells only)   Data format 
     Blood +  Avg. + strand total RNA-seq level of 68 blood experiments (tissues and primary cells only)   Data format 
     Blood -  Avg. - strand total RNA-seq level of 68 blood experiments (tissues and primary cells only)   Data format 
     Blood vessel +  Avg. + strand total RNA-seq level of 21 blood vessel experiments (tissues and primary cells only)   Data format 
     Blood vessel -  Avg. - strand total RNA-seq level of 21 blood vessel experiments (tissues and primary cells only)   Data format 
     Brain +  Avg. + strand total RNA-seq level of 127 brain experiments (tissues and primary cells only)   Data format 
     Brain -  Avg. - strand total RNA-seq level of 127 brain experiments (tissues and primary cells only)   Data format 
     Breast +  Avg. + strand total RNA-seq level of 4 breast experiments (tissues and primary cells only)   Data format 
     Breast -  Avg. - strand total RNA-seq level of 4 breast experiments (tissues and primary cells only)   Data format 
     Connective tissue +  Avg. + strand total RNA-seq level of 1 connective tissue experiments (tissues and primary cells only)   Data format 
     Connective tissue -  Avg. - strand total RNA-seq level of 1 connective tissue experiments (tissues and primary cells only)   Data format 
     Embryo +  Avg. + strand total RNA-seq level of 1 embryo experiments (tissues and primary cells only)   Data format 
     Embryo -  Avg. - strand total RNA-seq level of 1 embryo experiments (tissues and primary cells only)   Data format 
     Epithelium +  Avg. + strand total RNA-seq level of 1 epithelium experiments (tissues and primary cells only)   Data format 
     Epithelium -  Avg. - strand total RNA-seq level of 1 epithelium experiments (tissues and primary cells only)   Data format 
     Esophagus +  Avg. + strand total RNA-seq level of 5 esophagus experiments (tissues and primary cells only)   Data format 
     Esophagus -  Avg. - strand total RNA-seq level of 5 esophagus experiments (tissues and primary cells only)   Data format 
     Eye +  Avg. + strand total RNA-seq level of 1 eye experiments (tissues and primary cells only)   Data format 
     Eye -  Avg. - strand total RNA-seq level of 1 eye experiments (tissues and primary cells only)   Data format 
     Gallbladder +  Avg. + strand total RNA-seq level of 1 gallbladder experiments (tissues and primary cells only)   Data format 
     Gallbladder -  Avg. - strand total RNA-seq level of 1 gallbladder experiments (tissues and primary cells only)   Data format 
     Heart +  Avg. + strand total RNA-seq level of 36 heart experiments (tissues and primary cells only)   Data format 
     Heart -  Avg. - strand total RNA-seq level of 36 heart experiments (tissues and primary cells only)   Data format 
     Kidney +  Avg. + strand total RNA-seq level of 8 kidney experiments (tissues and primary cells only)   Data format 
     Kidney -  Avg. - strand total RNA-seq level of 8 kidney experiments (tissues and primary cells only)   Data format 
     Large intestine +  Avg. + strand total RNA-seq level of 15 large intestine experiments (tissues and primary cells only)   Data format 
     Large intestine -  Avg. - strand total RNA-seq level of 15 large intestine experiments (tissues and primary cells only)   Data format 
     Liver +  Avg. + strand total RNA-seq level of 9 liver experiments (tissues and primary cells only)   Data format 
     Liver -  Avg. - strand total RNA-seq level of 9 liver experiments (tissues and primary cells only)   Data format 
     Lung +  Avg. + strand total RNA-seq level of 20 lung experiments (tissues and primary cells only)   Data format 
     Lung -  Avg. - strand total RNA-seq level of 20 lung experiments (tissues and primary cells only)   Data format 
     Mouth +  Avg. + strand total RNA-seq level of 1 mouth experiments (tissues and primary cells only)   Data format 
     Mouth -  Avg. - strand total RNA-seq level of 1 mouth experiments (tissues and primary cells only)   Data format 
     Muscle +  Avg. + strand total RNA-seq level of 19 muscle experiments (tissues and primary cells only)   Data format 
     Muscle -  Avg. - strand total RNA-seq level of 19 muscle experiments (tissues and primary cells only)   Data format 
     Nerve +  Avg. + strand total RNA-seq level of 5 nerve experiments (tissues and primary cells only)   Data format 
     Nerve -  Avg. - strand total RNA-seq level of 5 nerve experiments (tissues and primary cells only)   Data format 
     Nose +  Avg. + strand total RNA-seq level of 1 nose experiments (tissues and primary cells only)   Data format 
     Nose -  Avg. - strand total RNA-seq level of 1 nose experiments (tissues and primary cells only)   Data format 
     Ovary +  Avg. + strand total RNA-seq level of 7 ovary experiments (tissues and primary cells only)   Data format 
     Ovary -  Avg. - strand total RNA-seq level of 7 ovary experiments (tissues and primary cells only)   Data format 
     Pancreas +  Avg. + strand total RNA-seq level of 8 pancreas experiments (tissues and primary cells only)   Data format 
     Pancreas -  Avg. - strand total RNA-seq level of 8 pancreas experiments (tissues and primary cells only)   Data format 
     Placenta +  Avg. + strand total RNA-seq level of 12 placenta experiments (tissues and primary cells only)   Data format 
     Placenta -  Avg. - strand total RNA-seq level of 12 placenta experiments (tissues and primary cells only)   Data format 
     Prostate +  Avg. + strand total RNA-seq level of 2 prostate experiments (tissues and primary cells only)   Data format 
     Prostate -  Avg. - strand total RNA-seq level of 2 prostate experiments (tissues and primary cells only)   Data format 
     Skin +  Avg. + strand total RNA-seq level of 11 skin experiments (tissues and primary cells only)   Data format 
     Skin -  Avg. - strand total RNA-seq level of 11 skin experiments (tissues and primary cells only)   Data format 
     Small intestine +  Avg. + strand total RNA-seq level of 4 small intestine experiments (tissues and primary cells only)   Data format 
     Small intestine -  Avg. - strand total RNA-seq level of 4 small intestine experiments (tissues and primary cells only)   Data format 
     Spinal cord +  Avg. + strand total RNA-seq level of 1 spinal cord experiments (tissues and primary cells only)   Data format 
     Spinal cord -  Avg. - strand total RNA-seq level of 1 spinal cord experiments (tissues and primary cells only)   Data format 
     Spleen +  Avg. + strand total RNA-seq level of 8 spleen experiments (tissues and primary cells only)   Data format 
     Spleen -  Avg. - strand total RNA-seq level of 8 spleen experiments (tissues and primary cells only)   Data format 
     Stomach +  Avg. + strand total RNA-seq level of 5 stomach experiments (tissues and primary cells only)   Data format 
     Stomach -  Avg. - strand total RNA-seq level of 5 stomach experiments (tissues and primary cells only)   Data format 
     Testis +  Avg. + strand total RNA-seq level of 2 testis experiments (tissues and primary cells only)   Data format 
     Testis -  Avg. - strand total RNA-seq level of 2 testis experiments (tissues and primary cells only)   Data format 
     Thyroid +  Avg. + strand total RNA-seq level of 5 thyroid experiments (tissues and primary cells only)   Data format 
     Thyroid -  Avg. - strand total RNA-seq level of 5 thyroid experiments (tissues and primary cells only)   Data format 
     Trachea +  Avg. + strand total RNA-seq level of 1 trachea experiments (tissues and primary cells only)   Data format 
     Trachea -  Avg. - strand total RNA-seq level of 1 trachea experiments (tissues and primary cells only)   Data format 
     Urinary bladder +  Avg. + strand total RNA-seq level of 2 urinary bladder experiments (tissues and primary cells only)   Data format 
     Urinary bladder -  Avg. - strand total RNA-seq level of 2 urinary bladder experiments (tissues and primary cells only)   Data format 
     Uterus +  Avg. + strand total RNA-seq level of 6 uterus experiments (tissues and primary cells only)   Data format 
     Uterus -  Avg. - strand total RNA-seq level of 6 uterus experiments (tissues and primary cells only)   Data format 
     Vagina +  Avg. + strand total RNA-seq level of 1 vagina experiments (tissues and primary cells only)   Data format 
     Vagina -  Avg. - strand total RNA-seq level of 1 vagina experiments (tissues and primary cells only)   Data format 
     Blood + (all biosamples)  Avg. + strand total RNA-seq level of 77 blood experiments (all biosamples)   Data format 
     Blood - (all biosamples)  Avg. - strand total RNA-seq level of 77 blood experiments (all biosamples)   Data format 
     Brain + (all biosamples)  Avg. + strand total RNA-seq level of 136 brain experiments (all biosamples)   Data format 
     Brain - (all biosamples)  Avg. - strand total RNA-seq level of 136 brain experiments (all biosamples)   Data format 
     Breast + (all biosamples)  Avg. + strand total RNA-seq level of 6 breast experiments (all biosamples)   Data format 
     Breast - (all biosamples)  Avg. - strand total RNA-seq level of 6 breast experiments (all biosamples)   Data format 
     Connective tissue + (all biosamples)  Avg. + strand total RNA-seq level of 3 connective tissue experiments (all biosamples)   Data format 
     Connective tissue - (all biosamples)  Avg. - strand total RNA-seq level of 3 connective tissue experiments (all biosamples)   Data format 
     Embryo + (all biosamples)  Avg. + strand total RNA-seq level of 8 embryo experiments (all biosamples)   Data format 
     Embryo - (all biosamples)  Avg. - strand total RNA-seq level of 8 embryo experiments (all biosamples)   Data format 
     Epithelium + (all biosamples)  Avg. + strand total RNA-seq level of 2 epithelium experiments (all biosamples)   Data format 
     Epithelium - (all biosamples)  Avg. - strand total RNA-seq level of 2 epithelium experiments (all biosamples)   Data format 
     Heart + (all biosamples)  Avg. + strand total RNA-seq level of 37 heart experiments (all biosamples)   Data format 
     Heart - (all biosamples)  Avg. - strand total RNA-seq level of 37 heart experiments (all biosamples)   Data format 
     Kidney + (all biosamples)  Avg. + strand total RNA-seq level of 10 kidney experiments (all biosamples)   Data format 
     Kidney - (all biosamples)  Avg. - strand total RNA-seq level of 10 kidney experiments (all biosamples)   Data format 
     Large intestine + (all biosamples)  Avg. + strand total RNA-seq level of 34 large intestine experiments (all biosamples)   Data format 
     Large intestine - (all biosamples)  Avg. - strand total RNA-seq level of 34 large intestine experiments (all biosamples)   Data format 
     Liver + (all biosamples)  Avg. + strand total RNA-seq level of 11 liver experiments (all biosamples)   Data format 
     Liver - (all biosamples)  Avg. - strand total RNA-seq level of 11 liver experiments (all biosamples)   Data format 
     Lung + (all biosamples)  Avg. + strand total RNA-seq level of 24 lung experiments (all biosamples)   Data format 
     Lung - (all biosamples)  Avg. - strand total RNA-seq level of 24 lung experiments (all biosamples)   Data format 
     Muscle + (all biosamples)  Avg. + strand total RNA-seq level of 26 muscle experiments (all biosamples)   Data format 
     Muscle - (all biosamples)  Avg. - strand total RNA-seq level of 26 muscle experiments (all biosamples)   Data format 
     Pancreas + (all biosamples)  Avg. + strand total RNA-seq level of 11 pancreas experiments (all biosamples)   Data format 
     Pancreas - (all biosamples)  Avg. - strand total RNA-seq level of 11 pancreas experiments (all biosamples)   Data format 
     Prostate + (all biosamples)  Avg. + strand total RNA-seq level of 4 prostate experiments (all biosamples)   Data format 
     Prostate - (all biosamples)  Avg. - strand total RNA-seq level of 4 prostate experiments (all biosamples)   Data format 
     Skin + (all biosamples)  Avg. + strand total RNA-seq level of 18 skin experiments (all biosamples)   Data format 
     Skin - (all biosamples)  Avg. - strand total RNA-seq level of 18 skin experiments (all biosamples)   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

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
adipose✓–
adrenal gland✓–
blood✓✓
blood vessel✓–
brain✓✓
breast✓✓
connective tissue✓✓
embryo✓✓
epithelium✓✓
esophagus✓–
eye✓–
gallbladder✓–
heart✓✓
kidney✓✓
large intestine✓✓
liver✓✓
lung✓✓
mouth✓–
muscle✓✓
nerve✓–
nose✓–
ovary✓–
pancreas✓✓
placenta✓–
prostate✓✓
skin✓✓
small intestine✓–
spinal cord✓–
spleen✓–
stomach✓–
testis✓–
thyroid✓–
trachea✓–
urinary bladder✓–
uterus✓–
vagina✓–

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/hg38/encode4/regulation/organAve/adiposePlus.bw stdout

Credits

Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Barbara Wold (Caltech) 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