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.
-These tracks complement one another and collectively provide a powerful resource for +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.
By default, the DNase (Layered), ATAC (Layered), H3K4me3 (Layered), H3K27ac (Layered), CTCF (Layered), and Transcription (Layered) tracks use a transparent overlay to visualize signals from multiple organs or tissues within a single track. For each organ or tissue, signal values from all associated experiments are averaged. Each organ or tissue is assigned a distinct color, 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 +track displays an overlay of representative organs: blood, brain, kidney, liver, and +muscle (the ATAC track has no kidney data). Clicking on the track opens a details page where you can view and select organs or tissues.
For the TF rPeaks track, each rPeak (representative peak) is colored in grayscale by the maximum ChIP-seq signal for the corresponding TF across all contributing biosamples (darker = higher signal, score 0 to 1,000). The HGNC gene symbol of the TF is displayed to the left when viewed in pack display mode. If the rPeak overlaps a cognate TF motif from a previously curated collection (Andrews et al., 2023), the motif site is colored green using decorators.
The TF ChIP-seq (Indiv.), DNase/ATAC/Histone/CTCF (Indiv.), and RNA-seq (Indiv.) tracks are hidden by default. Clicking on any of these tracks opens a details page where you can select specific biosample-level experiments to display.