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/geneimprint.html src/hg/makeDb/trackDb/human/hg38/geneimprint.html
index 3f85a63ec2c..fc7a1399f79 100644
--- src/hg/makeDb/trackDb/human/hg38/geneimprint.html
+++ src/hg/makeDb/trackDb/human/hg38/geneimprint.html
@@ -1,31 +1,27 @@
 <h2>Description</h2>
 
 <p>
-This track shows the human part of the Geneimprint catalog, with each gene
-placed on the genome. The catalog itself gives only a cytogenetic band, so the
+Part of the <a href="hgTrackUi?db=$db&amp;hgsid=${hgsid}&amp;g=$parentTrack">Imprinting</a> track collection, this track shows the human part of the Geneimprint
+catalog, with each gene placed on the genome. The catalog itself gives only a cytogenetic band, so the
 coordinates here come from resolving the gene symbols against the
 <a href="hgTrackUi?g=hgnc">HGNC</a> gene annotation. Note that the track
 contains all of the catalog, including 18 genes that Geneimprint records as
 <em>not</em> imprinted and 10 whose status is unknown. Use the filters on the
 track configuration page to narrow the display to the evidence levels you want.
 </p>
 
-<p>
-See the <a href="hgTrackUi?g=imprinting">Imprinting</a> track collection page for background on genomic imprinting and for the color scheme shared by all of its subtracks.
-</p>
-
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 Each item is one gene from the catalog, drawn over the span of the resolved
 locus. The item is labeled with the name Geneimprint uses, which for older
 entries can differ from today's approved symbol; the configuration page can
 switch the label to the approved symbol instead. Clicking an item opens a page
 with the imprint status, the expressed allele, the band the catalog gives, and
 links to the Geneimprint and HGNC entries.
 </p>
 
 <p>
 The color shows which parental copy is expressed:
 </p>