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/mouse/mm39/tads.html src/hg/makeDb/trackDb/mouse/mm39/tads.html deleted file mode 100644 index 01198453bf1..00000000000 --- src/hg/makeDb/trackDb/mouse/mm39/tads.html +++ /dev/null @@ -1,94 +0,0 @@ -<h2>Description</h2> -<p> -This track set displays <b>topologically associating domains (TADs)</b> in the mouse genome, -assembled from 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. -</p> -<p>The set contains three complementary sources, all <b>domain</b> calls:</p> -<ul> - <li><b>Dixon 2012 TADs</b> – the original TAD domains in mESC and cortex (lifted from mm9).</li> - <li><b>ENCODE contact domains</b> – uniformly called TAD domains across mouse biosamples - (Arrowhead/Hi-C), browsable by a faceted selector. Native mm10; lifted to mm39.</li> - <li><b>3D Genome Browser domains</b> – TAD domains across mouse Hi-C/Micro-C datasets, - exactly as called and published by the 3D Genome Browser, browsable by a faceted selector. - Native mm10; lifted to mm39.</li> -</ul> -<p> -The table below summarizes how each of these tracks' domains 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 (lifted from mm9)</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> -</table> -</blockquote> -<p> -The human counterpart of this track set (on hg38) additionally includes TAD <b>boundary</b> -tracks (Schmitt 2016, and a boundary-stability track); those datasets are human-only and have -no mouse equivalent, so the mouse set is domains only. -</p> - -<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 -regulatory loci. 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. This mouse set is domains only; to ask -whether a structural variant disrupts an insulating boundary, see the human (hg38) counterpart, -which adds dedicated TAD boundary 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 and resolutions produce different calls of the same underlying -biology. Domains are drawn as boxes spanning each self-interacting region. Calls native to an -earlier mouse assembly are lifted to the assembly being viewed (Dixon from mm9; ENCODE and the -3D Genome Browser from mm10 when viewed on mm39); the lift is noted in each track's long label. -The ENCODE and 3D Genome Browser tracks contain many biosamples and are browsable with a faceted -selector on their configuration pages. -</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 the 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/mm39/tad.txt" target="_blank">doc/mm39/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/mouse/mm39/tad.ra" target="_blank">trackDb/mouse/mm39/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> -</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> -</p>