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/hg38/tadsMcArthur.html src/hg/makeDb/trackDb/human/tadsMcArthur.html similarity index 55% rename from src/hg/makeDb/trackDb/human/hg38/tadsMcArthur.html rename to src/hg/makeDb/trackDb/human/tadsMcArthur.html index b812a69ba4c..ecdca0cbf66 100644 --- src/hg/makeDb/trackDb/human/hg38/tadsMcArthur.html +++ src/hg/makeDb/trackDb/human/tadsMcArthur.html @@ -3,60 +3,63 @@ 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". +Each boundary (about 100 kb) 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. </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 +<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>stable</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. +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 +<b>Default filter:</b> this track initially shows boundaries shared by at least +<b>4 of the 37 maps</b>. 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. +windows at both ends of every TAD. The genome was divided 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> +McArthur E, Capra JA. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/33545030" target="_blank"> +Topologically associating domain boundaries that are stable across diverse cell types are +evolutionarily constrained and enriched for heritability</a>. +<em>Am J Hum Genet</em>. 2021 Feb 4;108(2):269-283. +DOI: <a href="https://doi.org/10.1016/j.ajhg.2021.01.001" +target="_blank">10.1016/j.ajhg.2021.01.001</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/33545030" target="_blank">33545030</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7895846/" target="_blank">PMC7895846</a> </p>