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=$db&hgsid=${hgsid}&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>