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/human/hg19/tadsDixon.html src/hg/makeDb/trackDb/human/tadsDixon.html similarity index 62% rename from src/hg/makeDb/trackDb/human/hg19/tadsDixon.html rename to src/hg/makeDb/trackDb/human/tadsDixon.html index 945097f3056..d1e65032c71 100644 --- src/hg/makeDb/trackDb/human/hg19/tadsDixon.html +++ src/hg/makeDb/trackDb/human/tadsDixon.html @@ -1,44 +1,46 @@ <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. +Domains were called from Hi-C data analyzed in fixed-size 40 kb bins, so domain edges are +uncertain to roughly ±20 kb. Domains cover roughly 86–91% of the genome, and +the gaps between domains are what Dixon <em>et al.</em> call "topological +boundaries" (under 400 kb) or "unorganized chromatin" (over 400 kb). 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. </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> +<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>