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/doc/hg38/imprinting.txt src/hg/makeDb/doc/hg38/imprinting.txt index 53b5f82c702..8395c72dd00 100644 --- src/hg/makeDb/doc/hg38/imprinting.txt +++ src/hg/makeDb/doc/hg38/imprinting.txt @@ -223,30 +223,35 @@ # GeneScout coordinates are 1-based inclusive, so the start is decremented by # one. Established two ways: the export echoes whole chromosomes as # "chr1:1-248,956,422" (a 0-based system would start at 0), and comparing # genemap2.txt against the 0-based hgnc.bb over 17,617 genes gives a modal # start difference of exactly +1 and end difference of exactly 0. # # genemap2.txt is then used as an independent coordinate check: all 225 loci # with an OMIM gene entry agree with the licensed gene map exactly, 0 # disagreements on chromosome, start or end. bedToBigBed -type=bed9+6 -tab \ -as=$HOME/kent/src/hg/makeDb/scripts/imprinting/omimImprint.as \ -extraIndex=name \ omimImprint.bed /hive/data/genomes/hg38/chrom.sizes omimImprint.bb +# The OMIM curators confirmed that the (I) marker covers both established and +# candidate imprinted genes, and that the export gives no way to tell the two +# apart. The track labels and the description page say so; do not present these +# genes as settled imprinting calls. + # Check that the (I) marker really means imprinted, rather than being one of # GeneScout's display markers like the (S) that flags a gene spanning the edge # of a search interval. Compare the flagged loci with the two other subtracks, # against a size-matched random sample of unflagged genes as the baseline. cd /hive/data/genomes/hg38/bed/imprinting bedtools intersect -a omimImprint/omimImprint.bed -b akbari2023/akbariIdmr.bed -u | wc -l bedtools intersect -a omimImprint/omimImprint.bed -b geneimprint/geneimprint.bed -u | wc -l # 148 of the flagged loci overlap an Akbari iDMR and 303 overlap a Geneimprint # gene. For 529 randomly chosen genes that do NOT carry the marker the same two # counts are 0 and 5. The marker is also per gene, not per band: 11p15.5 has 13 # of its 129 genes flagged. # # No redistribution restriction applies: this track is built purely from the # GeneScout export and contains no OMIM download data, so unlike omimGene2 it