df99c448f8e0386bb718da0044b22752fc145713 gperez2 Thu Jun 4 00:15:12 2026 -0700 Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8". diff --git src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html index 493c7d5582d..0935cbb084c 100644 --- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html +++ src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html @@ -1,158 +1,157 @@ <h2>Description</h2> <p> This collection of tracks offers an integrated view of genomic annotations and experimental data from all phases of the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Project</a>, 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).</p> <p>Tracks labeled <b><em>(Layered)</em></b> show organ-averaged signals as a transparent overlay of multiple organs within a single track. Tracks labeled <b><em>(Indiv.)</em></b> show signals from individual experiments in specific biosamples.</p> <ul> -<li>The <b><em>H3K27ac (Layered)</em></b> track highlights a histone modification associated with -active enhancers and promoters, displayed as organ-averaged signal across 34 organs.</li> +<li>The <b><em>H3K27ac (Layered)</em></b> track displays enrichment levels of a histone modification associated with +active enhancers and promoters, averaged across 38 organs.</li> -<li>The <b><em>DNase (Layered)</em></b> track highlights regions of chromatin that are hypersensitive +<li>The <b><em>DNase (Layered)</em></b> 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 40 organs.</li> +across biosamples from the same organ for 41 organs.</li> -<li>The <b><em>ATAC (Layered)</em></b> track highlights regions of open chromatin identified by +<li>The <b><em>ATAC (Layered)</em></b> track displays regions of open chromatin identified by ATAC-seq, which uses Tn5 transposase insertion to assay accessibility. Signal is averaged -across 24 organs.</li> +across 26 organs.</li> -<li>The <b><em>H3K4me3 (Layered)</em></b> track highlights a histone modification associated with -active and poised promoters, displayed as organ-averaged signal across 35 organs.</li> +<li>The <b><em>H3K4me3 (Layered)</em></b> track displays enrichment levels of a histone modification associated with +active or poised promoters, averaged across 38 organs.</li> -<li>The <b><em>CTCF (Layered)</em></b> track highlights genomic regions bound by CTCF, a transcription -factor and architectural protein involved in chromatin organization and gene regulation. Signal -is averaged across 30 organs.</li> +<li>The <b><em>CTCF (Layered)</em></b> track displays genomic regions bound by CTCF, a multifunctional DNA-binding protein involved in chromatin organization and gene regulation. Signal +is averaged across 36 organs.</li> <li>The <b><em>Transcription (Layered)</em></b> track displays transcription levels measured by strand-specific total RNA-seq across a large number of biosamples, shown separately for the two genomic strands.</li> -<li>The <b><em>TF rPeaks</em></b> track shows genomic regions bound by TFs and other DNA-associated +<li>The <b><em>TF rPeaks</em></b> track displays genomic regions bound by TFs and other DNA-associated factors involved in transcriptional regulation, derived from ChIP-seq experiments profiling -911 factors across 1,152 biosamples.</li> +912 factors across 1,152 biosamples.</li> <li>The <b><em>TF ChIP-seq (Indiv.)</em></b>, <b><em>DNase/ATAC/Histone/CTCF (Indiv.)</em></b>, and <b><em>RNA-seq (Indiv.)</em></b> tracks display signals from individual experiments in specific biosamples.</li> </ul> <p> -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.</p> <p> 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 <a href="https://screen.wenglab.org/" target="_blank">SCREEN</a>.</p> <h2>Display Conventions</h2> <p> By default, the <b><em>DNase (Layered)</em></b>, <b><em>ATAC (Layered)</em></b>, <b><em>H3K4me3 (Layered)</em></b>, <b><em>H3K27ac (Layered)</em></b>, <b><em>CTCF (Layered)</em></b>, and <b><em>Transcription (Layered)</em></b> 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.</p> <p> For the <b><em>TF rPeaks</em></b> 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 <em>pack</em> display mode. If the rPeak overlaps a cognate TF motif from a previously curated collection (Andrews et al., 2023), the motif site is colored <span style="color:#36DD81; font-weight:bold;">green</span> using decorators.</p> <p> The <b><em>TF ChIP-seq (Indiv.)</em></b>, <b><em>DNase/ATAC/Histone/CTCF (Indiv.)</em></b>, and <b><em>RNA-seq (Indiv.)</em></b> 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.</p> <h2>Data Access</h2> <p> The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated download and analysis, the track data files can be downloaded from <a href="https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/regulation/" target="_blank">our download server</a> or queried using the <a href="../goldenPath/help/api.html" target="_blank">REST API</a>. Individual regions or the whole genome annotation can be accessed as text using our utilities <tt>bigWigToWig</tt> and <tt>bigBedToBed</tt>. Instructions for downloading source code and binaries can be found <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The original data files are also available from the <a href="https://www.encodeproject.org/" target="_blank">ENCODE portal</a>.</p> <h2>Credits</h2> <p> Data were generated by the ENCODE Consortium. The data were further processed for visualization through a collaborative effort between the <a href="https://www.umassmed.edu/zlab" target="_blank">Weng lab</a> and the <a href="https://sites.google.com/view/moore-lab/" target="_blank">Moore lab</a> at UMass Chan Medical School (funded by NIH grant HG012343). Integration and visualization were developed by Drs. Mingshi Gao, Greg Andrews, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center.</p> <h2>Data Use Policy</h2> <p> <b>Users may freely download, analyze, and publish results based on any ENCODE data without restrictions.</b> Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional.</p> <p> <b><em>Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE production laboratory(s) that generated the datasets used, as described in <a href="https://www.encodeproject.org/help/citing-encode/" target="_blank">Citing ENCODE</a>.</em></b></p> <h2>References</h2> <p> Andrews G, Fan K, Pratt HE, Phalke N, Zoonomia Consortium, Karlsson EK, Lindblad-Toh K, Weng Z. <a href="https://www.science.org/doi/10.1126/science.abn7930" target="_blank"> Mammalian evolution of human cis-regulatory elements and transcription factor binding sites</a>. <em>Science</em>. 2023;380(6643):eabn7930. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37104580" target="_blank">37104580</a> </p> <p> ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A <em>et al</em>. <a href="https://doi.org/10.1038/s41586-020-2493-4" target="_blank"> Expanded encyclopaedias of DNA elements in the human and mouse genomes</a>. <em>Nature</em>. 2020 Jul;583(7818):699-710. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32728249" target="_blank">32728249</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410828/" target="_blank">PMC7410828</a> </p> <p> Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y <em>et al</em>. <a href="https://www.nature.com/articles/s41586-025-09909-9" target="_blank"> An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation</a>. <em>Nature</em>. 2026 January 7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39763870" target="_blank">39763870</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11703161/" target="_blank">PMC11703161</a> </p>