691a2b8981d6db69e8707ea44041c4661cdac97e
max
  Wed Sep 9 06:38:29 2026 -0700
Imprinting: add the ASM Atlas tracks, and tidy the collection's labels

Adds a composite built from Rosenski et al. 2025, "Atlas of imprinted and
allele-specific DNA methylation in the human body". Three subtracks: the
458 regions whose methylation follows the parent of origin, the 72 known
control regions with the boundaries the paper redrew, and the pool of
385,235 regions carrying two methylation states that those came out of.
A fourth set, the regions whose methylation follows a nearby SNP, is
built by the scripts but its stanza is commented out, since sequence
driven methylation is not imprinting.

The authors released hg19 only, so all three are lifted. Their published
files are close to bare BED, so the SNPs, cell types, p-values, gene
links and gamete methylation on the details pages are read out of the
paper's supplementary tables and joined on by position. Regions that
lift but change length by more than 10%, because hg38 added sequence
inside them, are kept with a note rather than dropped: one of them is
TCEB3C, the only control region on chr18.

Also across the collection:
- long labels name their source right after "Imprinting", so that a
label read on its own says where the data came from
- the two gene catalogs are worded alike, and ordered OMIM, Geneimprint,
MethBase2, Akbari, ASM Atlas
- the OMIM curators confirmed that their (I) marker covers established
and candidate imprinted genes alike, with nothing in the export to
tell them apart. Labels, description page and makeDoc now say so, and
the claim that the set is "more conservative" than the computational
tracks is gone. The bigBed was rebuilt for the autoSql line, same 459
features.
- every subtrack page opens by naming the collection, linked back to
its hgTrackUi page, and no longer repeats the collection page's
introduction to imprinting

refs #37599

diff --git src/hg/makeDb/trackDb/human/hg38/imprinting.html src/hg/makeDb/trackDb/human/hg38/imprinting.html
index 4a21eaab7bf..6d2c59a5b03 100644
--- src/hg/makeDb/trackDb/human/hg38/imprinting.html
+++ src/hg/makeDb/trackDb/human/hg38/imprinting.html
@@ -10,51 +10,68 @@
 The regions that hold this asymmetry are called imprinting control regions, and
 a single one can govern the expression of a whole cluster of neighboring genes.
 Losing or gaining methylation at these regions is the cause of several
 developmental syndromes.
 </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.
+<a href="hgTrackUi?g=omimImprint">OMIM Genes</a> &mdash; the genes that the
+OMIM staff curate as imprinted or candidate imprinted, published through OMIM's
+GeneScout tool. The two are not distinguished in what OMIM publishes.
 </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
+<a href="hgTrackUi?g=geneimprint">Geneimprint Genes</a> &mdash; the genes that
+Geneimprint curates as imprinted or candidate imprinted, colored by which
 parental copy is expressed.
 </li>
 <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=akbariIdmr">Akbari iDMRs</a> &mdash; 192 imprinted
-differentially methylated regions compiled from five genome-wide studies,
-colored by which parental copy is methylated.
+differentially methylated regions that Akbari et al. 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.
+<a href="hgTrackUi?g=kaplanImprint">ASM Atlas</a> &mdash; three annotation
+sets from a survey of allele-specific methylation in about 40 purified cell
+types: regions whose methylation follows the parent of origin, known control
+regions with their boundaries redrawn, and the much larger pool of regions
+carrying two methylation states that these were drawn from.
 </li>
 </ul>
 
+<p>
+The first four sets above are gene or region catalogs assembled from the
+literature, so they overlap by design: a gene called imprinted by OMIM is
+usually also in Geneimprint, and its control region is usually among the Akbari
+iDMRs.
+The ASM Atlas is different in kind, since its regions were called from
+sequencing data rather than collected from papers, and most of them have never
+been linked to imprinting.
+</p>
+
 <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>