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/human/hg38/tadsEncode.html src/hg/makeDb/trackDb/human/hg38/tadsEncode.html new file mode 100644 index 00000000000..c3c86012a19 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/tadsEncode.html @@ -0,0 +1,80 @@ +<h2>Description</h2> +<p> +This composite shows <b>TAD domains</b> ("contact domains") called by the ENCODE +uniform Hi-C pipeline across <b>117 human biosamples</b> on hg38. 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> +ENCODE provides contact domains for many human biosamples across hundreds of files. This +track shows <b>one representative experiment per biosample</b>; by default a set of 14 +reference biosamples is displayed (GM12878, K562, HepG2, HCT116, IMR-90, A549, HL-60/S4, +heart left/right ventricle, dorsolateral prefrontal cortex, ovary, pancreas, transverse +colon, and motor neuron), and the remaining biosamples are turned off and reached through +the faceted selector. The complete set is available at the +<a href="https://www.encodeproject.org/search/?type=File&output_type=contact+domains&assembly=GRCh38" target="_blank">ENCODE portal</a>. +</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 likelihood that the spot is +a contact-domain corner); the details page also reports Arrowhead's upper/lower variance +and sign scores. These calls use a different algorithm and a finer resolution (5 kb, calling +sub-TAD contact domains) than the other TAD tracks, and are not directly comparable to them. +</p> +<p> +Use the faceted selector on the track configuration page to choose biosamples by +<b>Organ</b>, <b>Biosample type</b> (cell line, tissue, primary cell, in vitro +differentiated), <b>Assay</b> (intact or in situ Hi-C), <b>Life stage</b>, and +<b>Calls</b>. Where a biosample had both an untreated baseline and a perturbed (treated or +genetically modified) experiment, the baseline was chosen; a handful of biosamples that +exist only in a stimulated state (e.g. activated immune cells) are named accordingly. The +<b>Calls</b> facet distinguishes the 112 biosamples with native hg38 Arrowhead calls +("Arrowhead (hg38)") from 5 biosamples (LNCaP clone FGC, NCI-H460, RPMI7951, +SJCRH30, SK-N-MC) for which ENCODE provides only domains lifted from hg19 +("Lifted from hg19"); the lifted domains carry no Arrowhead scores. +</p> +<h2>Methods</h2> +<p> +Contact domains were produced by the ENCODE uniform Hi-C processing pipeline (developed by +the Aiden lab, built on Juicer), which calls domains with Arrowhead on GRCh38. For each +biosample, one representative experiment was selected (preferring native hg38 Arrowhead +calls, then an untreated baseline experiment over a perturbed one where both were available, +then the deepest experiment by assay type and data volume), and that +experiment's contact-domain files were pooled: each Juicer/Arrowhead paired-anchor BEDPE +record (in which both anchors describe the same domain interval) was reduced to a single +domain interval, the five Arrowhead scores were retained, and replicate calls whose +endpoints fell within one 5 kb bin were merged, keeping the call with the higher corner +score. The chosen ENCODE experiment accession is given in each subtrack's long label. +</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> +ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. +<em>Nature</em>. 2012;489(7414):57-74. +<a href="https://doi.org/10.1038/nature11247" target="_blank">doi:10.1038/nature11247</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>