76eabae1c28bb07c02af6a12fa9222c348b039d9 max Sun Sep 6 07:02:29 2026 -0700 DANIO-CODE: open each subtrack description with the sentence saying that the track is part of the DANIO-CODE container, linking to its hgTrackUi page, instead of burying it in a paragraph at the end of the description. refs #38265 diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/dcComp.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcComp.html index 835f07c808f..18d07cbc1c6 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/dcComp.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcComp.html @@ -1,169 +1,166 @@ <h2>Description</h2> <p> -This track holds the DANIO-CODE annotation of candidate regulatory elements, at five +This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> track collection. +It holds the consortium's annotation of candidate regulatory elements, at five developmental stages: Dome, 75% epiboly, 5-9 somites, Prim-5 and Long-pec. Four related annotations are shown for each stage. </p> <p> <b>ChromHMM</b> is a segmentation of the whole genome into ten chromatin states. The segmentation is learned from the combination of histone modifications present at each position, and each state was then given a name by hand, using the Roadmap Epigenomics annotation as a reference: active transcription start sites, their flanking regions, active and primed enhancers, poised elements, Polycomb-repressed regions and a quiescent state with no detectable mark. </p> <p> <b>PADREs</b> are predicted ATAC-supported developmental regulatory elements: the subset of the segmentation that also lies in a region of open chromatin, which is the consortium's set of candidate regulatory elements. Across all stages there are more than 140,000 of them. <b>cPADREs</b> are the consensus set of 83,553 elements that are called at every stage, so they can be compared position by position across development. <b>DOPEs</b> are dynamic orphan predicted elements: regions that are open at a given stage but carry no histone mark at all. </p> -<p> -This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> collection. -</p> - <h2>Display Conventions and Configuration</h2> <p> Each combination of annotation type and developmental stage is a separate track. On the configuration page they are laid out as a grid, with the annotation type across and the stage down. Only the ChromHMM tracks are checked when the grid is first opened. </p> <p> The ChromHMM and PADRE tracks are colored by chromatin state: </p> <table class="stdTbl"> <tr><th style="background-color:#A6CEE3;width:2em"> </th> <td>1_TssA1 — active transcription start site</td></tr> <tr><th style="background-color:#1F78B4;width:2em"> </th> <td>2_TssA2 — active transcription start site, second class</td></tr> <tr><th style="background-color:#33A02C;width:2em"> </th> <td>3_TssFlank1 — region flanking a transcription start site</td></tr> <tr><th style="background-color:#B2DF8A;width:2em"> </th> <td>4_TssFlank2 — region flanking a transcription start site, second class</td></tr> <tr><th style="background-color:#E31A1C;width:2em"> </th> <td>5_EnhA1 — active enhancer</td></tr> <tr><th style="background-color:#FB9A99;width:2em"> </th> <td>6_EnhFlank — region flanking an enhancer</td></tr> <tr><th style="background-color:#FF7F00;width:2em"> </th> <td>7_EnhWk1 — primed enhancer</td></tr> <tr><th style="background-color:#6A3D9A;width:2em"> </th> <td>8_Pois — poised element</td></tr> <tr><th style="background-color:#CAB2D6;width:2em"> </th> <td>9_ReprPC — Polycomb-repressed region</td></tr> <tr><th style="background-color:#A1A2A3;width:2em"> </th> <td>10_Quies — quiescent, no mark detected</td></tr> </table> <p> The DOPE tracks carry no state and are drawn in black. </p> <h2>Methods</h2> <p> The DANIO-CODE consortium assembled 1,802 zebrafish developmental genomics datasets, 1,438 of them already published and 366 generated by consortium members, and reprocessed all of them from the raw sequencing reads so that samples from different laboratories and different protocols can be compared with each other. ChIP-seq and ATAC-seq were run through the ENCODE pipelines, CAGE-seq through the FANTOM pipeline, and Hi-C and 4C-seq through the pipelines of the groups that produced them. The pipelines are published at <a href="https://gitlab.com/danio-code" target="_blank">gitlab.com/danio-code</a>, and samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. See Baranasic <em>et al</em>. 2022 for details. </p> <p> The genome was segmented with ChromHMM using the histone modification data in the <a href="hgTrackUi?g=dcChIPseqComposite">DC ChIP-seq</a> track, and the ten resulting states were named by comparison with the Roadmap Epigenomics annotation. Segments that overlap an ATAC-seq peak were kept as PADREs. The PADREs were then classified further by embedding their accessibility and histone signal with UMAP, which separates promoters from enhancers and brings out subclasses that follow the timing of their activity. Elements without any chromatin mark were split into those open at all stages and those open only at some; the second group is shown here as DOPEs, and both groups are shown pooled in the <a href="hgTrackUi?g=dcCopes_and_dopes">DC COPEs DOPEs</a> track. </p> <p> Element counts per stage, for PADREs: 85,750 at Dome, 93,394 at 75% epiboly, 123,324 at 5-9 somites, 122,462 at Prim-5 and 148,870 at Long-pec. For DOPEs: 4,896, 5,862, 7,384, 7,699 and 6,468 for the same stages. The consensus cPADRE set has 83,553 elements at every stage. </p> <p> At UCSC the tracks were converted from the consortium's public track hub at <a href="https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt" target="_blank"> trackhub2.genereg.net/DANIO-CODE</a> with the script <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/danioCode" target="_blank">danioCodeHubToRa.py</a>, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/danRer11/danioCode.txt" target="_blank">our makeDoc</a>. </p> <h2>Data Access</h2> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>dcComp</i>. </p> <p> For automated download and analysis, the annotations are stored in bigBed files that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/" target="_blank">our download server</a>. Files are named after the stage and the annotation type, for example <tt>Prim5_PADREs.bb</tt>, <tt>Prim5_ChromHMM.bb</tt>, <tt>Prim5_cPADRE.bb</tt> and <tt>Prim5_DOPEs.bb</tt>. The stage names in the file names are Dome, Epi75, Hpf12, Prim5 and LongPec. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain features within a given range, for example </p> <pre>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/Prim5_PADREs.bb \ -chrom=chr1 -start=20000000 -end=20100000 stdout</pre> <p> The original data files, and the sample and protocol metadata behind them, are available from the DANIO-CODE data coordination center at <a href="https://danio-code.zfin.org" target="_blank">danio-code.zfin.org</a> and from the consortium's track hub at <a href="https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt" target="_blank"> trackhub2.genereg.net/DANIO-CODE</a>. </p> <h2>Credits</h2> <p> Thanks to the DANIO-CODE consortium for collecting, reprocessing and publishing these data, and to the laboratories that produced the original datasets. </p> <h2>References</h2> <p> Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N <em>et al</em>. <a href="https://doi.org/10.1038/s41588-022-01089-w" target="_blank"> Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- regulatory elements</a>. <em>Nat Genet</em>. 2022 Jul;54(7):1037-1050. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35789323" target="_blank">35789323</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279159/" target="_blank">PMC9279159</a> </p>