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/tadsSchmitt.html src/hg/makeDb/trackDb/human/tadsSchmitt.html similarity index 57% rename from src/hg/makeDb/trackDb/human/hg38/tadsSchmitt.html rename to src/hg/makeDb/trackDb/human/tadsSchmitt.html index 006a6eb2176..6d37a6f3edb 100644 --- src/hg/makeDb/trackDb/human/hg38/tadsSchmitt.html +++ src/hg/makeDb/trackDb/human/tadsSchmitt.html @@ -1,44 +1,48 @@ <h2>Description</h2> <p> This composite shows <b>TAD boundaries</b> across 21 human samples (7 cell lines and 14 primary tissues) from Schmitt <em>et al.</em>, 2016. A boundary is the insulating region that separates two adjacent topologically associating domains. These are <em>boundaries</em>, not domains; for domain intervals see the Dixon 2012 TADs track. </p> <h2>Display Conventions and Configuration</h2> <p> -Each boundary is a 40 kb bin; the bin width reflects the localization precision of the -40 kb analysis, not a measured physical width. Subtracks are grouped by sample type -(cell line vs. primary tissue) and organ system, and colored by organ system. Because the -same boundary is reported independently per sample, turning on multiple subtracks lets you -read boundary conservation directly: a boundary present in many samples is constitutive, -while one present in few is cell-type specific. By default a representative subset of -samples is shown. +Each boundary is a bin of about 40 kb, the fixed segment size used in the Hi-C analysis. The +bin width reflects the localization precision of the analysis, not a measured physical +width. Subtracks are grouped by sample type (cell line vs. primary tissue) and organ system, +and colored by organ system. Because the same boundary is reported independently per sample, +turning on multiple subtracks shows boundary conservation directly: a boundary present in +many samples is stable across cell types, while one present in few is cell-type specific. By +default, 5 samples are shown: GM12878, H1, IMR90, dorsolateral prefrontal cortex, and liver. </p> <h2>Methods</h2> <p> Boundaries were called with the insulation-score method at 40 kb resolution (1 Mb insulation square, 200 kb delta window) as described in Schmitt <em>et al.</em>, 2016 (Supplementary Table S3). Per-sample boundary bins were obtained on assembly hg19; for this assembly they were used natively or lifted with the UCSC <b>liftOver</b> tool, with a small fraction of bins that did not map cleanly 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> -Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B. -A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human -Genome. <em>Cell Rep</em>. 2016;17(8):2042-2059. -<a href="https://doi.org/10.1016/j.celrep.2016.10.061" target="_blank">doi:10.1016/j.celrep.2016.10.061</a> +Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/27851967" target="_blank"> +A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome</a>. +<em>Cell Rep</em>. 2016 Nov 15;17(8):2042-2059. +DOI: <a href="https://doi.org/10.1016/j.celrep.2016.10.061" +target="_blank">10.1016/j.celrep.2016.10.061</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/27851967" target="_blank">27851967</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478386/" target="_blank">PMC5478386</a> </p>