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/scripts/imprinting/kaplanParentalAsm.as src/hg/makeDb/scripts/imprinting/kaplanParentalAsm.as new file mode 100644 index 00000000000..7d7d6a56f5b --- /dev/null +++ src/hg/makeDb/scripts/imprinting/kaplanParentalAsm.as @@ -0,0 +1,29 @@ +table kaplanParentalAsm +"Regions whose methylation follows the parent of origin rather than the DNA sequence (Rosenski et al. 2025)" + ( + string chrom; "Reference sequence chromosome or scaffold" + uint chromStart; "Start position in chromosome" + uint chromEnd; "End position in chromosome" + string name; "Control region name, or the imprinted gene the region sits next to" + uint score; "Not used, always 0" + char[1] strand; "Not applicable, always ." + uint thickStart; "Start of where display should be thick" + uint thickEnd; "End of where display should be thick" + uint itemRgb; "Colour by the gamete in which the methylation mark is laid down" + string regionType; "Region type|a known imprinting control region, a new region beside a known imprinted gene, or a region reported for the first time here" + string icrType; "Type|germline DMR methylated in the oocyte or in sperm, or a DMR that acquires its methylation after fertilisation" + string icrName; "Control region|name of the known imprinting control region this region corresponds to" + lstring icrGenes; "Control region genes|imprinted genes linked to that control region in the literature" + lstring imprintedGenes; "Imprinted genes nearby|known imprinted genes within 200 kb" + lstring snps; "ASM SNPs|dbSNP identifiers of the heterozygous SNPs used to phase the two alleles" + uint snpCount; "SNP count|number of such SNPs in the region" + lstring alleles; "Alleles|the two alleles of each SNP" + lstring cellTypes; "Cell types|cell types in which allele-specific methylation was seen" + uint cellTypeCount; "Cell type count|number of cell types supporting the region" + string minAdjP; "Best adjusted p|smallest adjusted p-value over the SNPs and cell types of the region" + string methOocyte; "Methylation in oocyte|mean methylation of the region in published oocyte methylomes" + string methSperm; "Methylation in sperm|mean methylation of the region in published sperm methylomes" + string methIcm; "Methylation in inner cell mass|mean methylation of the region in the inner cell mass" + string methBlastocyst; "Methylation in blastocyst|mean methylation of the region in the blastocyst" + string liftNote; "Lifting note|set when hg38 inserted sequence inside the region, so that its boundaries no longer match the published hg19 ones" + )