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/wgEncodeReg4TfPeaks.html src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html index b040c8fd4c3..fb9e60a7dde 100644 --- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html +++ src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html @@ -1,173 +1,173 @@ <h2>Description</h2> <p>This track displays representative ChIP-seq peaks (rPeaks) and detected DNA motif sites for regulatory regions in the human genome, identified using ENCODE ChIP-seq data across all phases of the project. The regions are bound by DNA-associated proteins involved in transcriptional regulation, including RNA polymerase, transcription factors (TFs), and chromatin remodeling proteins. Sequence-specific TFs bind directly to short DNA motifs via their DNA-binding domains, while other proteins associate indirectly through interactions with sequence-specific TFs. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a high-throughput method used to map genome-wide protein-DNA interactions. Regions with high ChIP-seq signal (peaks) frequently contain binding sites for the assayed protein. For each DNA-associated protein, ChIP-seq peaks from all ENCODE biosamples were integrated to define a set of representative peaks (rPeaks). For detailed information on individual factors and their motifs, see <a target="_blank" href="https://factorbook.org">Factorbook.org</a>.</p> <h2>Display Conventions and Configuration</h2> <p>Each rPeak is colored in grayscale by maximum ChIP-seq signal across contributing biosamples (darker = higher signal, score 0 to 1,000):</p> <table> <thead> <tr> <th style="border-bottom: 2px solid #6678B1;">Color</th> <th style="border-bottom: 2px solid #6678B1;">Score</th> </tr> </thead> <tr> <th bgcolor="#000000"></th> <th align="left">1000 (highest signal)</th> </tr> <tr> <th bgcolor="#393939"></th> <th align="left">750</th> </tr> <tr> <th bgcolor="#717171"></th> <th align="left">500</th> </tr> <tr> <th bgcolor="#AAAAAA"></th> <th align="left">250</th> </tr> <tr> <th bgcolor="#E3E3E3"></th> <th align="left">1 (lowest signal)</th> </tr> </table> <p>Low-scoring peaks appear in very light gray by default; the <b>Shade of lowest-scoring items</b> setting can darken them for easier visibility. <b>Note:</b> Increasing the shade reduces the visible contrast between low and high scoring peaks.</p> <p>If the rPeak overlaps a cognate TF motif site from the collection in Andrews et al., 2023, the motif site is colored <span style="color:#36DD81; font-weight:bold;">green</span> using decorators.</p> <p>Clicking on an rPeak provides detailed information about the biosamples where the rPeak was detected, including the count of biosamples with contributing ChIP-seq peaks, the total number of biosamples assayed for the protein, and a per-biosample table listing each contributing experiment with its ENCODE accession. The protein name links to <a target="_blank" href="https://factorbook.org">Factorbook</a>, and overlapping ENCODE candidate cis-regulatory elements (cCREs) link to <a target="_blank" href="https://screen.wenglab.org">SCREEN</a>.</p> -<p>By default, rPeaks for all 911 DNA-associated proteins with ENCODE ChIP-seq data are +<p>By default, rPeaks for all 912 DNA-associated proteins with ENCODE ChIP-seq data are displayed. A filter is available to select specific proteins.</p> <h2>Methods</h2> -<p>2,502 ENCODE ChIP-seq experiments were integrated from 911 DNA-associated proteins across +<p>2,509 ENCODE ChIP-seq experiments were integrated from 912 DNA-associated proteins across 1,152 unique biosamples to produce representative peaks (rPeaks) for each protein. The processing steps were as follows:</p> <ol> <li>ChIP-seq peaks for each protein were downloaded from the <a target="_blank" href="https://www.encodeproject.org">ENCODE Portal</a>, generated using the <a target="_blank" href="https://www.encodeproject.org/chip-seq/transcription_factor/">ENCODE Transcription Factor ChIP-seq Processing Pipeline</a>.</li> <li>Using bedtools merge, ChIP-seq peaks were clustered from the protein’s experiments across all biosamples.</li> <li>In each cluster, the peak with the highest ChIP signal (normalized by sequencing depth) was selected as the rPeak.</li> <li>All ChIP-seq peaks overlapping this rPeak by at least one nucleotide were marked as represented and removed from subsequent clustering rounds.</li> <li>Steps 2-4 were repeated until a final list of non-overlapping rPeaks was generated, representing all ChIP-seq peaks for the protein.</li> </ol> <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 genome annotation is stored in bigBed files that can be downloaded from <a href="https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/regulation/" target="_blank">our download server</a>. The data may also be explored interactively using our <a href="../goldenPath/help/api.html" target="_blank">REST API</a>. The original data files are also available from the <a href="https://www.encodeproject.org/" target="_blank">ENCODE portal</a>.</p> <p> These files may also be locally explored using our tool <tt>bigBedToBed</tt>, 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 <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain features confined to a given range, e.g., <br><br> <tt>bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/regulation/tfRpeak/TFrPeakClusters.bb stdout</tt></p> <h2>Credits</h2> <p>This track was made possible by the efforts of the ENCODE Consortium, ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating and processing the ChIP-seq datasets. The ENCODE accession numbers for the constituent datasets are accessible from the peak details page. The data were generated by the following production labs: Drs. Bradley Bernstein (Broad), John Stamatoyannopoulos (UW), Kevin Struhl (HMS), Kevin White (UChicago), Michael Snyder (Stanford), Peggy Farnham (USC), Richard Myers (HAIB), Sherman Weissman (Yale), Tim Reddy (Duke), Vishwanath Iyer (UTA), and Xiang-Dong Fu (UCSD).</p> <p>The data were further processed for visualization through a collaborative effort between the <a target="_blank" href="https://www.umassmed.edu/zlab">Weng lab</a> and the <a target="_blank" href="https://sites.google.com/view/moore-lab/">Moore lab</a> at UMass Chan Medical School (funded by NIH grant HG012343). Special thanks to Drs. Mingshi Gao, Greg Andrews, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were members of the ENCODE Data Analysis Center, for developing this track, including providing the rPeak and motif datasets and associated metadata and building the track.</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> <p> Pratt HE, Andrews GR, Phalke N, Huey JD, Purcaro MJ, van der Velde A, Moore JE, Weng Z. <a href="https://doi.org/10.1093/nar/gkab1039" target="_blank"> Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites</a>. <em>Nucleic Acids Research</em>. 2022;50(D1):D141-D149. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34747468" target="_blank">34747468</a> </p>