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/tadsDixon.html src/hg/makeDb/trackDb/mouse/mm10/tadsDixon.html new file mode 100644 index 00000000000..3729283c09f --- /dev/null +++ src/hg/makeDb/trackDb/mouse/mm10/tadsDixon.html @@ -0,0 +1,46 @@ +<h2>Description</h2> +<p> +This composite shows the original mouse <b>topologically associating domain (TAD)</b> calls +from Dixon et al. 2012, the study that defined TADs. Two cell types are shown: mouse +embryonic stem cells (mESC) and mouse cortex. TADs are self-interacting genomic regions +whose boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and +constrain enhancer-promoter contacts. +</p> +<p> +The calls were made on mm9 and are displayed here lifted to this assembly (see Methods). +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Each domain is drawn as a box spanning a self-interacting region. The two cell types are +separate subtracks. Domains were called on 40 kb-binned Hi-C data, so domain edges are +uncertain to roughly the bin size; domains do not tile the genome end to end. +</p> + +<h2>Methods</h2> +<p> +TAD domains were called by Dixon et al. 2012 with the directionality-index hidden Markov +model at 40 kb resolution (the published "Combined" replicate call set: 2,200 mESC +and 1,518 cortex domains, mm9). UCSC lifted the mm9 coordinates to this assembly with +<b>liftOver</b> (a small percentage of domains that did not map cleanly were dropped) and +reformatted them to bigBed; no re-calling was performed. +</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>