22fc293ddc00fce956d75fbcdb237e5d19d08fd5 max Thu Sep 3 14:39:29 2026 -0700 Three more Imprinting subtracks on hg38: Geneimprint, Akbari iDMRs, OMIM Geneimprint: the human catalog of imprinted and candidate imprinted genes from geneimprint.com, 274 genes. The catalog gives only a cytogenetic band, so symbols are resolved against the HGNC track, with fallbacks for small RNA clusters and for symbols HGNC has retired. Akbari iDMRs: the 192 imprinted differentially methylated regions that Akbari et al. 2023 (PMID 36777186) compiled from five genome-wide studies. Their published coordinates are 1-based inclusive, not bed, as their own PatMat reader shows, so the starts are shifted. OMIM: the 459 loci that OMIM curates as imprinted. That call is published only through GeneScout and is in no OMIM download file, so the input is a GeneScout export made by hand from a browser. OMIM phenotype entries, which are mapped disease regions up to 90 Mb rather than gene positions, are left out. Also unifies the color scheme across the collection, so vermillion always means the maternal copy, blue the paternal copy and gray no parent of origin, and relates the collection to the Human Methylation Atlas. refs #37599 diff --git src/hg/makeDb/trackDb/human/hg38/imprinting.html src/hg/makeDb/trackDb/human/hg38/imprinting.html index 24323e1c11a..4a21eaab7bf 100644 --- src/hg/makeDb/trackDb/human/hg38/imprinting.html +++ src/hg/makeDb/trackDb/human/hg38/imprinting.html @@ -14,23 +14,71 @@ </p> <p> This collection brings together annotations that mark imprinted loci and the allele-specific methylation that defines them. </p> <h2>Subtracks</h2> <ul> <li> <a href="hgTrackUi?g=methBaseAsm">MethBase2 ASM</a> — for every CpG site, the fraction of MethBase2 human methylomes in which the site was part of an allelically methylated region. Peaks mark candidate imprinting control regions. </li> +<li> +<a href="hgTrackUi?g=geneimprint">Geneimprint</a> — the human part of the +Geneimprint catalog of imprinted and candidate imprinted genes, colored by which +parental copy is expressed. +</li> +<li> +<a href="hgTrackUi?g=akbariIdmr">Akbari iDMRs</a> — 192 imprinted +differentially methylated regions compiled from five genome-wide studies, +colored by which parental copy is methylated. +</li> +<li> +<a href="hgTrackUi?g=omimImprint">OMIM Imprinted</a> — the genes that +the OMIM staff have curated as imprinted, published through OMIM's GeneScout +tool. +</li> </ul> +<p> +DNA methylation itself is annotated elsewhere in the browser rather than here. +The Kaplan lab human methylation atlas, which gives methylation and +unmethylated regions for a large panel of purified cell types, is a separate +track: +<a href="hgTrackUi?g=humanMethylationAtlasSummary">Human Methylation Atlas +Summary</a>, under DNA Methylation. +</p> + +<h2>Color Conventions</h2> + +<p> +The subtracks share one color scheme, so a color means the same thing +throughout the collection: +</p> + +<table class="stdTbl"> + <tr><th style="background-color:#D55E00;width:2em"> </th> + <td>The maternal copy is the one the annotation marks</td></tr> + <tr><th style="background-color:#0072B2;width:2em"> </th> + <td>The paternal copy is the one the annotation marks</td></tr> + <tr><th style="background-color:#555555;width:2em"> </th> + <td>The annotation carries no parent of origin</td></tr> +</table> + +<p> +What is being marked differs by subtrack, because the sources annotate +different things: Geneimprint names the copy that is <em>expressed</em>, while +the iDMR track names the copy that is <em>methylated</em>. So H19 is vermillion +in one and blue in the other, and both are correct. Each subtrack page states +which copy its colors refer to, and adds any categories that only it uses. +</p> + <h2>Data Access</h2> <p> Each subtrack has its own description page with the details on how the data was made and how to download and intersect the annotations. Use the links above. </p>