b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 gperez2 Wed Sep 30 14:17:50 2026 -0700 Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599 diff --git src/hg/makeDb/trackDb/mouse/mm10/tadsDixon.html src/hg/makeDb/trackDb/mouse/tadsDixon.html similarity index 72% rename from src/hg/makeDb/trackDb/mouse/mm10/tadsDixon.html rename to src/hg/makeDb/trackDb/mouse/tadsDixon.html index 3729283c09f..c12ce5a6493 100644 --- src/hg/makeDb/trackDb/mouse/mm10/tadsDixon.html +++ src/hg/makeDb/trackDb/mouse/tadsDixon.html @@ -1,46 +1,49 @@ <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. +The two cell types are separate subtracks. Domains were called from Hi-C data analyzed in +fixed-size 40 kb bins, so domain edges are uncertain to roughly ±20 kb, and domains +do not cover the whole genome. </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> +<a href="https://www.ncbi.nlm.nih.gov/pubmed/22495300" target="_blank"> +Topological domains in mammalian genomes identified by analysis of chromatin interactions</a>. +<em>Nature</em>. 2012 Apr 11;485(7398):376-80. +DOI: <a href="https://doi.org/10.1038/nature11082" target="_blank">10.1038/nature11082</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/22495300" target="_blank">22495300</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356448/" target="_blank">PMC3356448</a> </p>