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/tads3dgb.html src/hg/makeDb/trackDb/human/hg38/tads3dgb.html index e5569ed45bd..84a53ff1d48 100644 --- src/hg/makeDb/trackDb/human/hg38/tads3dgb.html +++ src/hg/makeDb/trackDb/human/hg38/tads3dgb.html @@ -1,49 +1,47 @@ <h2>Description</h2> <p> This composite shows <b>TAD domains</b> from the -<a href="http://3dgenome.fsm.northwestern.edu/" target="_blank">3D Genome Browser</a> -(3DGB) across <b>464 human Hi-C and Micro-C datasets</b> on hg38. Each subtrack is one -3DGB dataset, displayed exactly as called and published by 3DGB. TAD domains are -megabase-scale regions of the genome that preferentially self-interact; their boundaries -(frequently bound by CTCF and cohesin) insulate neighboring regions and constrain -enhancer-promoter contacts. +<a href="http://3dgenome.fsm.northwestern.edu/" target="_blank">3D Genome Browser</a> (3DGB) +across <b>464 human Hi-C and Micro-C datasets</b> on hg38. Each subtrack is one 3DGB +dataset, displayed exactly as called and published by 3DGB. TAD domains are regions of the +genome, typically hundreds of kilobases to about a megabase, that preferentially +self-interact. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring +regions and constrain enhancer-promoter contacts. </p> <p> The 464 datasets span a wide range of normal and cancer samples, baseline and perturbation conditions, organs, and cell types, drawn from many published studies and re-processed by 3DGB through a single TAD-calling pipeline. They are browsable with a <b>faceted selector</b> (see below); the displayed domain intervals are 3DGB's own, with no UCSC re-calling, merging, lifting, or recurrence scoring. </p> <h2>Display Conventions and Configuration</h2> <p> -Each subtrack is drawn as boxes spanning the self-interacting domains and is -<b>colored by organ</b>. By default a small set of canonical reference datasets is shown -(GM12878, H1-ESC, IMR-90, and HMEC); all other datasets are turned off and can be enabled -through the faceted selector. Mousing over a domain shows the dataset name, organ, and -assay. +Each subtrack is <b>colored by organ</b>. By default a small set of canonical reference +datasets is shown (GM12878, H1-ESC, IMR-90, and HMEC). All other datasets are turned off and +can be enabled through the faceted selector. Mousing over a domain shows the dataset name, +organ, and assay. </p> <p> These 464 datasets are <b>not a cross-comparable consensus</b>. Each represents one dataset's own TAD calls, made by different laboratories on different samples; coordinates -are therefore not directly comparable across subtracks, and they are not directly -comparable to the other TAD tracks in this set (which use different callers and -resolutions). Because calls are made on binned Hi-C data (3DGB calls TADs at 25 kb), -domain edges are uncertain to roughly the bin size, and domains do not tile the genome end -to end. +are therefore not directly comparable across subtracks, and they are not directly comparable +to the other TAD tracks in this set (which use different callers and resolutions). Because +3DGB calls TADs from Hi-C data analyzed in fixed-size 20 or 25 kb bins, domain edges are +only accurate to roughly one bin, and domains do not cover the whole genome. </p> <h3>Faceted selector</h3> <p> Use the faceted selector on the track configuration page to choose which datasets to display. Datasets can be filtered by: </p> <ul> <li><b>Organ</b> – the organ of the sample (used for subtrack color).</li> <li><b>Cell type</b> – the cell type, where annotated by 3DGB ("(unspecified)" when 3DGB does not record one).</li> <li><b>Assay</b> – Hi-C or Micro-C.</li> <li><b>Condition</b> – whether the sample is normal or cancer.</li> <li><b>Treatment</b> – baseline (untreated) or perturbation (e.g. drug treatment, gene knockout, or other experimental manipulation).</li> @@ -54,31 +52,31 @@ <h3>The "Provenance" facet</h3> <p> Because this track ships every 3DGB human dataset, a few of the underlying source studies are <b>already represented elsewhere in the UCSC Genome Browser</b>. The Provenance facet flags these so they can be identified or filtered out: </p> <ul> <li><b>Novel to browser</b> (422 datasets) – the source study is not otherwise displayed in the UCSC Genome Browser.</li> <li><b>Also in another UCSC track</b> (42 datasets) – the underlying Hi-C study is already represented elsewhere in the UCSC Genome Browser, either as its own track or as an input to another track in this TAD set. These include Schmitt 2016 (11 datasets, also shown directly as the <b>Schmitt 2016 boundaries</b> track here), Rao 2014 (7 datasets; the Rao 2014 Hi-C maps are also offered in the browser), a few ENCODE - datasets (overlapping the <b>ENCODE contact domains</b> track), and several studies + datasets (overlapping the <b>ENCODE TADs</b> track), and several studies (e.g. Dixon 2015) that are inputs to the <b>TAD boundary stability</b> track rather than displayed individually. The flag is intended to help avoid double-counting; it does not imply each dataset is separately viewable elsewhere.</li> </ul> <p> To view only datasets that are new to the browser, select "Novel to browser" in the Provenance facet. Note that even the "Also in another UCSC track" datasets may differ in their displayed coordinates from the other UCSC tracks, because 3DGB re-processed and re-called each study through its own pipeline. </p> <h2>Methods</h2> <p> TAD domains were called by the 3D Genome Browser pipeline and are displayed verbatim. UCSC performed only a format normalization: each 3DGB per-dataset TAD file (a BED-like @@ -102,26 +100,35 @@ The complete original datasets are available from the <a href="http://3dgenome.fsm.northwestern.edu/" target="_blank">3D Genome Browser</a>. </p> <h2>Credits</h2> <p> Thanks to the 3D Genome Browser team (Yue lab, Northwestern University) for assembling and uniformly processing these datasets. The 3D Genome Browser data are distributed under a <a href="https://creativecommons.org/licenses/by-nc/4.0/" target="_blank">CC BY-NC 4.0</a> license (free for non-commercial use). Please cite the 3D Genome Browser, and the original studies, when using these data. </p> <h2>References</h2> <p> -Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F. -The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D -genome architecture. <em>Nucleic Acids Res</em>. 2026;54(D1):D48-D54. -<a href="https://doi.org/10.1093/nar/gkaf1109" target="_blank">doi:10.1093/nar/gkaf1109</a> +Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, Li D, Choudhary MNK, Li Y, Hu M <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/30286773" target="_blank"> +The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range +chromatin interactions</a>. +<em>Genome Biol</em>. 2018 Oct 4;19(1):151. +DOI: <a href="https://doi.org/10.1186/s13059-018-1519-9" +target="_blank">10.1186/s13059-018-1519-9</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/30286773" target="_blank">30286773</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172833/" target="_blank">PMC6172833</a> </p> <p> -Wang Y, Song F, Zhang B, Zhang L, <em>et al.</em> -The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and -long-range chromatin interactions. <em>Genome Biol</em>. 2018;19(1):151. -<a href="https://doi.org/10.1186/s13059-018-1519-9" target="_blank">doi:10.1186/s13059-018-1519-9</a> +Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/41206958" target="_blank"> +The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome +architecture</a>. +<em>Nucleic Acids Res</em>. 2026 Jan 6;54(D1):D48-D54. +DOI: <a href="https://doi.org/10.1093/nar/gkaf1109" target="_blank">10.1093/nar/gkaf1109</a>; PMID: +<a href="https://www.ncbi.nlm.nih.gov/pubmed/41206958" target="_blank">41206958</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12807788/" target="_blank">PMC12807788</a> </p>