17b7d3c37be41135afaf8e91e365e3847af96ca5 lrnassar Mon Jun 22 10:56:56 2026 -0700 Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt). diff --git src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.html src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.html new file mode 100644 index 00000000000..511abca9a7e --- /dev/null +++ src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.html @@ -0,0 +1,68 @@ +<h2>Description</h2> +<p> +This composite shows <b>TAD domains</b> ("contact domains") called by the ENCODE +uniform Hi-C pipeline across <b>16 mouse biosamples</b>. Contact domains are regions that +preferentially self-interact, called by the Arrowhead algorithm (Juicer). Each subtrack is +one biosample, browsable with a <b>faceted selector</b> (filter by organ, biosample type, +assay, life stage, and call type). +</p> +<p> +The calls are native to mm10. On mm39 they are shown lifted from mm10 (noted in each track's +long label); the "Calls" facet records the native call assembly. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Each domain is drawn as a box, and subtracks are <b>colored by organ</b>. Mousing over a +domain shows the biosample and the Arrowhead corner score; the details page also reports +Arrowhead's upper/lower variance and sign scores. Use the faceted selector on the track +configuration page to choose biosamples by <b>Organ</b>, <b>Biosample type</b>, <b>Assay</b> +(intact or in situ Hi-C), <b>Life stage</b>, and <b>Calls</b>. These calls use a different +algorithm and finer resolution (5 kb sub-TAD contact domains) than the Dixon domains and are +not directly comparable to them. +</p> + +<h2>Methods</h2> +<p> +Contact domains were produced by the ENCODE uniform Hi-C processing pipeline (Aiden lab, +built on Juicer), which calls domains with Arrowhead. For each biosample, one representative +experiment was selected (preferring an untreated baseline over a perturbed experiment where +both were available) and its contact-domain files were pooled: each Juicer/Arrowhead +paired-anchor BEDPE record (both anchors describing the same domain interval) was reduced to a +single domain interval, the five Arrowhead scores retained, and replicate calls whose +endpoints fell within one 5 kb bin merged (keeping the higher corner score). For mm39, the +mm10 domains were lifted with <b>liftOver</b>. The chosen ENCODE experiment accession is given +in each subtrack's long label and links to the ENCODE portal. +</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>. +The complete dataset is available at the +<a href="https://www.encodeproject.org/search/?type=File&output_type=contact+domains&assembly=mm10" target="_blank">ENCODE portal</a>. +</p> + +<h2>References</h2> +<p> +ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, <em>et al.</em> +Perspectives on ENCODE. <em>Nature</em>. 2020;583(7818):693-698. +<a href="https://doi.org/10.1038/s41586-020-2449-8" target="_blank">doi:10.1038/s41586-020-2449-8</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> +</p> +<p> +Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. +Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. +<em>Cell Syst</em>. 2016;3(1):95-8. +<a href="https://doi.org/10.1016/j.cels.2016.07.002" target="_blank">doi:10.1016/j.cels.2016.07.002</a> +</p>