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/tadsDixon.html src/hg/makeDb/trackDb/human/hg38/tadsDixon.html new file mode 100644 index 00000000000..945097f3056 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/tadsDixon.html @@ -0,0 +1,44 @@ +<h2>Description</h2> +<p> +This track shows <b>topologically associating domains (TADs)</b>, the original +"topological domains" defined by Dixon <em>et al.</em> 2012, in two human +cell types: H1 human embryonic stem cells (hESC) and IMR90 fetal lung fibroblasts. A +domain is a contiguous region that preferentially interacts with itself in Hi-C data. +</p> +<h2>Display Conventions and Configuration</h2> +<p> +Each domain is drawn as a box. Domains were called on 40 kb-binned Hi-C data, so domain +edges are uncertain to roughly ±20 kb and all coordinates fall on a 40 kb grid. +Domains cover roughly 86–91% of the genome; they do not tile end to end, and +the gaps between boxes are Dixon's "boundary" (<400 kb) or "unorganized +chromatin" (>400 kb) regions. No per-domain confidence score is published by the +authors, so none is shown. These coordinates are not directly comparable to the other TAD +tracks, which use different callers. +</p> +<h2>Methods</h2> +<p> +Domains were identified with a directionality-index hidden Markov model on 40 kb Hi-C +contact matrices (Dixon <em>et al.</em>, 2012). The published combined-replicate domain +calls (Supplementary Table S3) were obtained for hESC and IMR90, originally on assembly +hg18/NCBI36, and lifted to this assembly with the UCSC <b>liftOver</b> tool; a small +fraction of domains that did not map cleanly were dropped. +</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>