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/tadsMcArthur.html src/hg/makeDb/trackDb/human/hg38/tadsMcArthur.html new file mode 100644 index 00000000000..b812a69ba4c --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/tadsMcArthur.html @@ -0,0 +1,62 @@ +<h2>Description</h2> +<p> +This track shows <b>TAD boundary stability</b>: for each 100 kb genomic window, how many of +37 cell-type contact maps place a TAD boundary there (McArthur & Capra, 2021). +Boundaries shared by many cell types are evolutionarily constrained and enriched for +complex-trait heritability. +</p> +<p> +<b>This is a derived, cross-study summary, not a primary set of TAD calls.</b> The 37 maps +were uniformly re-processed (via the 3D Genome Browser, using the Dixon directionality +pipeline) from five earlier studies (Rao 2014, Dixon 2015, Leung 2015, Schmitt 2016, and +ENCODE cancer cell lines); 9 of those contexts overlap the Schmitt boundaries track in +this set, so the two are not independent. The input maps were called at heterogeneous +resolution (25 kb for the Rao-lab set, 40 kb for the others). +</p> +<h2>Display Conventions and Configuration</h2> +<p> +Each 100 kb "bookend" boundary bin is shaded by the number of cell-type maps +sharing it (1–37): darker indicates a boundary shared by more cell types. Use the +<b>filter</b> to show only boundaries shared by at least a chosen number of maps. We +describe these as <em>recurrent across N of 37 maps</em>, not "conserved". +</p> +<p> +<b>Interpreting the score:</b> the score counts how many independent cell-type maps agree on a +boundary, which serves as a confidence measure. High values mark <b>constitutive</b> boundaries +shared across cell types: the most reliable, and enriched for CTCF binding and evolutionary +constraint. Boundaries seen in only one or a few maps are largely cell-type-specific. Raising the +filter yields a smaller, higher-confidence set of boundaries. +</p> +<p> +<b>Default filter:</b> this track initially shows boundaries shared by at least <b>4 of the 37 +maps</b>. Boundaries seen in only 1–3 maps are no more CTCF-enriched or evolutionarily +constrained than expected by chance. Lower the <b>filter</b> (minimum maps) to 1 to display all +boundaries. +</p> +<h2>Methods</h2> +<p> +TAD boundaries from 37 re-processed cell-type maps were each represented as the 100 kb +windows flanking every TAD ("bookend" boundaries); the genome was tiled into +100 kb windows and, for each window, the number of maps with a boundary in it was counted +(McArthur & Capra, 2021). Data were obtained from the authors' repository on assembly +hg19 and lifted to this assembly with the UCSC <b>liftOver</b> tool where needed. +</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> +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> +</p>