b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 gperez2 Wed Sep 30 14:17:50 2026 -0700 Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599 diff --git src/hg/makeDb/trackDb/human/hg38/tads.html src/hg/makeDb/trackDb/human/hg38/tads.html index 948a9c937d6..ed33ba1da9e 100644 --- src/hg/makeDb/trackDb/human/hg38/tads.html +++ src/hg/makeDb/trackDb/human/hg38/tads.html @@ -1,128 +1,132 @@ <h2>Description</h2> <p> This track set displays <b>topologically associating domains (TADs)</b> and TAD -<b>boundaries</b> in the human genome, assembled from several published Hi-C studies. -TADs are self-interacting regions of the genome, typically hundreds of kilobases -to about a megabase, and themselves nested, with smaller contact domains contained within -larger top-level TADs. Their boundaries (frequently bound by CTCF and cohesin) insulate -neighboring regions and constrain enhancer-promoter contacts. Disruption of a TAD boundary -can rewire gene regulation and cause disease, and TADs are widely used to nominate candidate -target genes for non-coding variants. +<b>boundaries</b> in the human genome, assembled from several published Hi-C studies. TADs +are self-interacting regions of the genome, typically hundreds of kilobases to about a +megabase. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring +regions and constrain enhancer-promoter contacts. </p> <p>The set contains five complementary sources:</p> <ul> <li><b>Dixon 2012 TADs</b> – the original TAD <em>domains</em> in hESC and IMR90 cells (lifted from hg18).</li> - <li><b>ENCODE contact domains</b> – uniformly called TAD <em>domains</em> across 117 - ENCODE human biosamples (hg38 only), browsable by a faceted selector (organ, biosample - type, assay). These are finer-resolution (5 kb) sub-TAD contact domains.</li> - <li><b>3D Genome Browser domains</b> – TAD <em>domains</em> across 464 human + <li><b>ENCODE TADs</b> – TAD <em>domains</em> across 117 ENCODE human biosamples (hg38 + only), 112 of them called with Arrowhead by the ENCODE uniform Hi-C pipeline, browsable + by a faceted selector (organ, biosample type, assay, life stage, calls). The Arrowhead + calls are finer-resolution (5 kb) contact domains, smaller than the Dixon TADs.</li> + <li><b>3D Genome Browser</b> – TAD <em>domains</em> across 464 human Hi-C/Micro-C datasets (normal and cancer, baseline and perturbation), exactly as called and published by the 3D Genome Browser, browsable by a faceted selector - (organ, cell type, assay, condition, treatment, year, study).</li> + (organ, cell type, assay, condition, treatment, provenance, year, study).</li> <li><b>Schmitt 2016 boundaries</b> – TAD <em>boundaries</em> across 21 human tissues and cell lines.</li> <li><b>TAD boundary stability</b> – how recurrent each boundary is across 37 cell-type maps (McArthur & Capra 2021).</li> </ul> <p> The table below summarizes how each source's domains or boundaries were called and at what resolution: </p> <blockquote> <table border=1 class='stdTbl'> <tr><th>Track</th><th>Feature</th><th>Calling method</th><th>Resolution</th></tr> <tr><td>Dixon 2012</td><td>Domains</td><td>Directionality-index HMM</td><td>40 kb</td></tr> -<tr><td>ENCODE contact domains</td><td>Domains</td><td>Arrowhead (Juicer), ENCODE uniform Hi-C pipeline</td><td>5 kb</td></tr> -<tr><td>3D Genome Browser 2.0</td><td>Domains</td><td>Resource's own per-dataset TAD calls, shown verbatim</td><td>25 kb</td></tr> +<tr><td>ENCODE TADs</td><td>Domains</td><td>Arrowhead (Juicer), ENCODE uniform Hi-C pipeline (112 of 117 biosamples)</td><td>5 kb</td></tr> +<tr><td>3D Genome Browser 2.0</td><td>Domains</td><td>Resource's own per-dataset TAD calls, shown verbatim</td><td>20 or 25 kb</td></tr> <tr><td>Schmitt 2016</td><td>Boundaries</td><td>Insulation score</td><td>40 kb</td></tr> <tr><td>McArthur & Capra 2021</td><td>Boundaries (stability)</td><td>Boundary sharing across 37 reprocessed cell-type maps</td><td>100 kb windows</td></tr> </table> </blockquote> -<h2>How to use these tracks</h2> -<p> -The <b>domain</b> tracks (Dixon, ENCODE, 3D Genome Browser) answer "are my variant -and a candidate gene in the same TAD?" and help prioritize target genes at -non-coding GWAS loci. The <b>boundary</b> tracks (Schmitt, stability) answer "does my -structural variant disrupt an insulating boundary?" and help interpret -the regulatory impact of deletions, duplications, and inversions. Because the domain tracks -are nested (ENCODE calls smaller sub-TAD contact domains; Dixon and the 3D Genome Browser -call larger top-level TADs), "which TAD?" is answered at different scales by -different tracks. -</p> - <h2>Display Conventions and Configuration</h2> <p> -Each source is shown as a separate track because TAD calls are <b>not directly -comparable across studies</b>: different algorithms (directionality index/HMM, -insulation score, Arrowhead) and resolutions (5–100 kb) produce different calls -of the same underlying biology. <b>Domains</b> are drawn as boxes spanning each -self-interacting region; <b>boundaries</b> are drawn as the short bins that divide -adjacent domains. Because calls are made on binned data, domain edges are uncertain to -roughly the caller's bin size (from a few kilobases for the ENCODE 5 kb calls up to about -±50 kb for the 100 kb stability bins), and the bin width of a boundary feature -reflects this localization precision, not a measured physical width. Domains do not -tile the genome end to end; the gaps between domain boxes are inter-domain or unorganized -regions, not display artifacts. The <b>ENCODE</b> and <b>3D Genome Browser</b> tracks each -contain many biosamples and are browsable with a faceted selector on their track -configuration pages; a small default set is shown and the rest are enabled through the -facets. +Each source is shown as a separate track because TAD calls are <b>not directly comparable +across studies</b>: different algorithms (directionality index/HMM, insulation score, +Arrowhead) and resolutions (5–100 kb) produce different calls of the same underlying +biology. Because TADs are called from Hi-C data analyzed in fixed-size bins, domain edges +are uncertain to roughly the bin size (from a few kilobases for the ENCODE 5 kb calls up to +about ±50 kb for the 100 kb stability windows), and the width of a boundary reflects +this precision, not a measured physical width. Domains do not cover the whole genome, and +the gaps between domains are inter-domain or unorganized regions, not display artifacts. The +<b>ENCODE</b> and <b>3D Genome Browser</b> tracks each contain many biosamples and are +browsable with a faceted selector on their track configuration pages. A small default set is +shown and the rest are enabled through the facets. </p> <h2>Methods</h2> <p> Each source was called independently by its original study or resource; the calling method and resolution for each are summarized in the table in the Description above. See the individual subtrack description pages for full methods, source publications, and assembly/liftOver details for each dataset. </p> <p> The UCSC source for this track set is available on GitHub: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/tad.txt" target="_blank">doc/hg38/tad.txt</a> (makedoc), <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/tad" target="_blank">makeDb/scripts/tad</a> (build scripts), and <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/hg38/tad.ra" target="_blank">trackDb/human/hg38/tad.ra</a> (trackDb). </p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="hgTables" target="_blank">Table Browser</a> or the <a href="hgIntegrator" target="_blank">Data Integrator</a>. For programmatic access, the track can be accessed using the Genome Browser's <a href="https://genome.ucsc.edu/goldenPath/help/api.html" target="_blank">REST API</a>. The underlying bigBed files can be downloaded from our <a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/tad/" target="_blank">download server</a>. </p> <h2>References</h2> <p> Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. -Topological domains in mammalian genomes identified by analysis of chromatin -interactions. <em>Nature</em>. 2012;485(7398):376-80. -<a href="https://doi.org/10.1038/nature11082" target="_blank">doi:10.1038/nature11082</a> +<a href="https://www.ncbi.nlm.nih.gov/pubmed/22495300" target="_blank"> +Topological domains in mammalian genomes identified by analysis of chromatin interactions</a>. +<em>Nature</em>. 2012 Apr 11;485(7398):376-80. +DOI: <a href="https://doi.org/10.1038/nature11082" target="_blank">10.1038/nature11082</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/22495300" target="_blank">22495300</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356448/" target="_blank">PMC3356448</a> </p> <p> -McArthur E, Capra JA. Topologically associating domain boundaries that are stable across -diverse cell types are evolutionarily constrained and enriched for heritability. -<em>Am J Hum Genet</em>. 2021;108(2):269-283. -<a href="https://doi.org/10.1016/j.ajhg.2021.01.001" target="_blank">doi:10.1016/j.ajhg.2021.01.001</a> +McArthur E, Capra JA. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/33545030" target="_blank"> +Topologically associating domain boundaries that are stable across diverse cell types are +evolutionarily constrained and enriched for heritability</a>. +<em>Am J Hum Genet</em>. 2021 Feb 4;108(2):269-283. +DOI: <a href="https://doi.org/10.1016/j.ajhg.2021.01.001" +target="_blank">10.1016/j.ajhg.2021.01.001</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/33545030" target="_blank">33545030</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7895846/" target="_blank">PMC7895846</a> </p> <p> -Rao SS, Huntley MH, Durand NC, Stamenova EK, <em>et al.</em> -A 3D map of the human genome at kilobase resolution reveals principles of chromatin -looping. <em>Cell</em>. 2014;159(7):1665-80. -<a href="https://doi.org/10.1016/j.cell.2014.11.021" target="_blank">doi:10.1016/j.cell.2014.11.021</a> +Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, +Lander ES <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/25497547" target="_blank"> +A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping</a>. +<em>Cell</em>. 2014 Dec 18;159(7):1665-80. +DOI: <a href="https://doi.org/10.1016/j.cell.2014.11.021" +target="_blank">10.1016/j.cell.2014.11.021</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/25497547" target="_blank">25497547</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635824/" target="_blank">PMC5635824</a> </p> <p> -Schmitt AD, Hu M, Jung I, Xu Z, <em>et al.</em> -A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human -Genome. <em>Cell Rep</em>. 2016;17(8):2042-2059. -<a href="https://doi.org/10.1016/j.celrep.2016.10.061" target="_blank">doi:10.1016/j.celrep.2016.10.061</a> +Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/27851967" target="_blank"> +A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome</a>. +<em>Cell Rep</em>. 2016 Nov 15;17(8):2042-2059. +DOI: <a href="https://doi.org/10.1016/j.celrep.2016.10.061" +target="_blank">10.1016/j.celrep.2016.10.061</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/27851967" target="_blank">27851967</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478386/" target="_blank">PMC5478386</a> </p> <p> Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F. -The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D -genome architecture. <em>Nucleic Acids Res</em>. 2026;54(D1):D48-D54. -<a href="https://doi.org/10.1093/nar/gkaf1109" target="_blank">doi:10.1093/nar/gkaf1109</a> +<a href="https://www.ncbi.nlm.nih.gov/pubmed/41206958" target="_blank"> +The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome +architecture</a>. +<em>Nucleic Acids Res</em>. 2026 Jan 6;54(D1):D48-D54. +DOI: <a href="https://doi.org/10.1093/nar/gkaf1109" target="_blank">10.1093/nar/gkaf1109</a>; PMID: +<a href="https://www.ncbi.nlm.nih.gov/pubmed/41206958" target="_blank">41206958</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12807788/" target="_blank">PMC12807788</a> </p>