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/wgEncodeReg4TfChip.html src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html index b087f4c105b..8dab1a0a973 100644 --- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html +++ src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html @@ -1,183 +1,183 @@ <h2>Description</h2> <p>This track displays genome-wide binding profiles of DNA-associated proteins from 2,503 individual ENCODE ChIP-seq experiments, which form the experimental basis for the TF rPeaks track. These proteins include transcription factors (TFs), RNA polymerase, and chromatin-associated proteins involved in transcriptional regulation. Sequence-specific TFs bind directly to DNA motifs via DNA-binding domains, while others interact indirectly through protein-protein interactions. ChIP-seq (chromatin immunoprecipitation followed by sequencing) enables genome-wide mapping of protein-DNA interactions. Each ChIP-seq experiment is shown as two subtracks:</p> <ul> <li><b>Signal</b> - a bigWig track of the experiment's signal</li> <li><b>Peak</b> - a bigBed track of the experiment's peaks, colored in grayscale by ChIP-seq signal (darker = higher signal, score 0 to 1,000): <table style="margin-left: 30px;"> <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> </li> </ul> <p>Peaks often correspond to protein binding sites in specific biosamples. Additional ChIP-seq datasets can be explored through the <a target="_blank" href="https://www.encodeproject.org/">ENCODE portal</a>.</p> <h2>Display Conventions and Configuration</h2> <p>Click a specific protein target and organ/tissue combination to view available datasets. -Subtracks can be further filtered by Tf, Organ, Biosample Type, Life Stage, and Data +Subtracks can be further filtered by TF, Organ, Biosample Type, Life Stage, and Data Type (Signal or Peak).</p> <p>Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ.</p> <table cellspacing="0" cellpadding="4" style="margin-top: 0.5em; border-collapse: collapse;"> <tr> <td style="background-color:rgb(255,119,39); padding:4px 12px; border:1px solid #666;">adipose</td> <td style="background-color:rgb(90,179,68); padding:4px 12px; border:1px solid #666;">adrenal gland</td> <td style="background-color:rgb(254,75,173); padding:4px 12px; border:1px solid #666;">blood</td> <td style="background-color:rgb(255,37,41); padding:4px 12px; border:1px solid #666;">blood vessel</td> </tr> <tr> <td style="background-color:rgb(121,147,150); padding:4px 12px; border:1px solid #666;">bone</td> <td style="background-color:rgb(2,199,185); padding:4px 12px; border:1px solid #666;">bone marrow</td> <td style="background-color:rgb(155,155,18); padding:4px 12px; border:1px solid #666;">brain</td> <td style="background-color:rgb(65,171,173); padding:4px 12px; border:1px solid #666;">breast</td> </tr> <tr> <td style="background-color:rgb(138,135,169); padding:4px 12px; border:1px solid #666;">connective tissue</td> <td style="background-color:rgb(118,158,101); padding:4px 12px; border:1px solid #666;">embryo</td> <td style="background-color:rgb(221,126,107); padding:4px 12px; border:1px solid #666;">epithelium</td> <td style="background-color:rgb(159,131,100); padding:4px 12px; border:1px solid #666;">esophagus</td> </tr> <tr> <td style="background-color:rgb(163,127,144); padding:4px 12px; border:1px solid #666;">eye</td> <td style="background-color:rgb(116,50,165); padding:4px 12px; border:1px solid #666;">heart</td> <td style="background-color:rgb(92,161,153); padding:4px 12px; border:1px solid #666;">kidney</td> <td style="background-color:rgb(86,86,36); padding:4px 12px; border:1px solid #666;">large intestine</td> </tr> <tr> <td style="background-color:rgb(137,152,82); padding:4px 12px; border:1px solid #666;">liver</td> <td style="background-color:rgb(130,163,45); padding:4px 12px; border:1px solid #666;">lung</td> <td style="background-color:rgb(6,218,147); padding:4px 12px; border:1px solid #666;">lymphoid tissue</td> <td style="background-color:rgb(130,141,158); padding:4px 12px; border:1px solid #666;">mouth</td> </tr> <tr> <td style="background-color:rgb(137,135,170); padding:4px 12px; border:1px solid #666;">muscle</td> <td style="background-color:rgb(160,156,0); padding:4px 12px; border:1px solid #666;">nerve</td> <td style="background-color:rgb(161,126,151); padding:4px 12px; border:1px solid #666;">ovary</td> <td style="background-color:rgb(175,100,41); padding:4px 12px; border:1px solid #666;">pancreas</td> </tr> <tr> <td style="background-color:rgb(0,176,240); padding:4px 12px; border:1px solid #666;">parathyroid gland</td> <td style="background-color:rgb(20,74,159); padding:4px 12px; border:1px solid #666;">penis</td> <td style="background-color:rgb(104,171,71); padding:4px 12px; border:1px solid #666;">placenta</td> <td style="background-color:rgb(140,140,140); padding:4px 12px; border:1px solid #666;">prostate</td> </tr> <tr> <td style="background-color:rgb(127,133,209); padding:4px 12px; border:1px solid #666;">skin</td> <td style="background-color:rgb(98,98,41); padding:4px 12px; border:1px solid #666;">small intestine</td> <td style="background-color:rgb(130,141,158); padding:4px 12px; border:1px solid #666;">spinal cord</td> <td style="background-color:rgb(136,157,97); padding:4px 12px; border:1px solid #666;">spleen</td> </tr> <tr> <td style="background-color:rgb(145,144,99); padding:4px 12px; border:1px solid #666;">stomach</td> <td style="background-color:rgb(139,140,140); padding:4px 12px; border:1px solid #666;">testis</td> <td style="background-color:rgb(27,119,58); padding:4px 12px; border:1px solid #666;">thyroid</td> <td style="background-color:rgb(186,111,165); padding:4px 12px; border:1px solid #666;">uterus</td> </tr> <tr> <td style="background-color:rgb(255,101,174); padding:4px 12px; border:1px solid #666;">vagina</td> <td></td> <td></td> <td></td> </tr> </table> <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>. Clicking any accession in the track's configuration table links directly to the corresponding file details page on the ENCODE portal.</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://encode-public.s3.amazonaws.com/2020/12/04/ddd64b54-7aad-4a2d-9270-ce677581b64b/ENCFF492SKF.bigBed stdout</tt></p> <h2>Credits</h2> <p>Data were generated by the ENCODE Consortium through 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). 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.</p> <h2>References</h2> <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>