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/omimImprintToBed.py src/hg/makeDb/scripts/imprinting/omimImprintToBed.py index ac1434739db..ece71575ac2 100755 --- src/hg/makeDb/scripts/imprinting/omimImprintToBed.py +++ src/hg/makeDb/scripts/imprinting/omimImprintToBed.py @@ -1,22 +1,24 @@ #!/usr/bin/env python3 """ -Build a bed9+ file of the genes that OMIM curates as imprinted. +Build a bed9+ file of the genes that OMIM curates as imprinted or candidate +imprinted. The OMIM staff curate imprinting from the primary literature, but that call is published only through GeneScout, which appends "(I)" to the coordinates in its -Location column. It is in neither the OMIM gene map nor any OMIM download file, +Location column. The curators say the marker covers established and candidate +imprinted genes alike, and the export does not separate the two. It is in neither the OMIM gene map nor any OMIM download file, so the input is a GeneScout results table exported by hand from a browser (genescout.omim.org sits behind a bot challenge that blocks scripted downloads). See the makeDoc for the exact search. Everything comes from that one export. Its coordinates are on GRCh38, 1-based and inclusive, so the start of each interval is decremented by one. GeneScout lists OMIM phenotype entries alongside genes. Those are mapped disease regions, not loci: they run up to 90 Mb and would cover the whole display, so they are dropped and listed in the report. They are recognised without needing any other file, because a phenotype entry repeats the same MIM number in the Gene MIM# and the Phenotype MIM# columns, while a gene entry carries two different numbers. Usage: