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//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/hg19/tads.html src/hg/makeDb/trackDb/human/hg19/tads.html new file mode 100644 index 00000000000..8a0703ca0f8 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg19/tads.html @@ -0,0 +1,90 @@ +

Description

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+This track set displays topologically associating domains (TADs) and TAD +boundaries in the human genome, assembled from published Hi-C studies. TADs are +self-interacting regions of the genome, typically hundreds of kilobases to about a megabase, +and themselves nested, with smaller contact domains contained within larger top-level TADs. +Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and +constrain enhancer-promoter contacts. Disruption of a TAD boundary can rewire gene regulation +and cause disease, and TADs are widely used to nominate candidate target genes for non-coding +variants. +

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The set contains three complementary sources:

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Two further domain sources are available on the hg38 assembly:

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How to Use These Tracks

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+The domain track (Dixon) answers "are my variant and a candidate gene in the +same TAD?" and helps prioritize target genes at non-coding GWAS loci. The +boundary tracks (Schmitt, stability) answer "does my structural variant disrupt +an insulating boundary?" and help interpret the regulatory impact of deletions, +duplications, and inversions. +

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Display Conventions and Configuration

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+Each source is shown as a separate track because TAD calls are not directly comparable +across studies: different algorithms (directionality index/HMM, insulation score) and +resolutions (40–100 kb) produce different calls of the same underlying biology. +Domains are drawn as boxes spanning each self-interacting region; boundaries +are drawn as the short bins that divide adjacent domains. Because calls are made on binned +data, domain edges are uncertain to roughly the caller's bin size, and the bin width of a +boundary feature reflects this localization precision, not a measured physical width. Domains +do not tile the genome end to end; the gaps between domain boxes are inter-domain or +unorganized regions, not display artifacts. +

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Methods

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+See the individual subtrack description pages for full methods, source publications, and +assembly/liftOver details for each dataset. In brief: Dixon domains were called with the +directionality-index HMM at 40 kb (lifted from hg18); Schmitt boundaries with the +insulation-score method at 40 kb; and the boundary-stability track counts, per 100 kb window, +how many of 37 re-processed cell-type maps share a boundary (McArthur & Capra 2021). The +Schmitt and stability tracks are native to hg19. +

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Data Access

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+The raw data can be explored interactively with the +Table Browser or the +Data Integrator. For programmatic access, the +track can be accessed using the Genome Browser's +REST API. +The underlying bigBed files can be downloaded from our +download server. +

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References

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+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. Nature. 2012;485(7398):376-80. +doi:10.1038/nature11082 +

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+McArthur E, Capra JA. Topologically associating domain boundaries that are stable across +diverse cell types are evolutionarily constrained and enriched for heritability. +Am J Hum Genet. 2021;108(2):269-283. +doi:10.1016/j.ajhg.2021.01.001 +

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+Schmitt AD, Hu M, Jung I, Xu Z, et al. +A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human +Genome. Cell Rep. 2016;17(8):2042-2059. +doi:10.1016/j.celrep.2016.10.061 +