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> &mdash; 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> &mdash; 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> &mdash; 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> &mdash; 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">&nbsp;</th>
+      <td>The maternal copy is the one the annotation marks</td></tr>
+  <tr><th style="background-color:#0072B2;width:2em">&nbsp;</th>
+      <td>The paternal copy is the one the annotation marks</td></tr>
+  <tr><th style="background-color:#555555;width:2em">&nbsp;</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>