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 @@ -1,46 +1,43 @@ <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>