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/akbariIdmr.html src/hg/makeDb/trackDb/human/hg38/akbariIdmr.html index 0602fff1eeb..6cda526d548 100644 --- src/hg/makeDb/trackDb/human/hg38/akbariIdmr.html +++ src/hg/makeDb/trackDb/human/hg38/akbariIdmr.html @@ -1,44 +1,43 @@ <h2>Description</h2> <p> -An imprinted differentially methylated region, or iDMR, is a stretch of the genome where the CpG sites of one parental copy are methylated and the same sites on the other copy are not. Because the methylated copy is always the one from the same parent, an iDMR is a fixed landmark that says which of a person's two chromosomes came from the mother and which from the father, without sequencing the parents. +Part of the <a href="hgTrackUi?db=$db&hgsid=${hgsid}&g=$parentTrack">Imprinting</a> track collection, this track shows imprinted differentially methylated +regions, or iDMRs. Because the methylated copy of an iDMR is always the one from the same parent, +an iDMR is a fixed landmark that says which of a person's two chromosomes came from the mother and +which from the father, without sequencing the parents. </p> <p> This track shows 192 such regions on the autosomes, assembled by Akbari et al. (2023) from five earlier genome-wide surveys of imprinted methylation and used by their PatMat method to assign whole chromosomes to a parent of origin. Just under half of the regions were reported independently by two or more of the five studies. The rest come from a single study and were kept only after they showed the expected half-methylated signal in public methylomes from blood and from many tissues. The X chromosome was left out, since it is not generally thought to carry iDMRs. </p> <p> The regions cover the classic imprinting control regions, including the H19 region and both IGF2 DMRs on chromosome 11, KvDMR1 at the KCNQ1 cluster, the SNRPN region on chromosome 15, the IG-DMR and MEG3 regions on chromosome 14 and both GNAS regions on chromosome 20, together with a long tail of less well-established loci. </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 region. Items are labeled with the first gene at or near the region; the configuration page can switch the label to the full list of genes, which is also shown when the mouse hovers over an item. The regions have no meaningful strand. </p> <p> The color shows which parental copy carries the methylation. Vermillion and blue mean the maternal and the paternal copy on every subtrack of this collection, but what is marked differs: this track marks the <em>methylated</em> copy, while <a href="hgTrackUi?g=geneimprint">Geneimprint</a> marks the <em>expressed</em> copy. At the H19 region this track is blue because the