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/imprinting.ra src/hg/makeDb/trackDb/human/hg38/imprinting.ra index 94a70e856f0..37970bfb851 100644 --- src/hg/makeDb/trackDb/human/hg38/imprinting.ra +++ src/hg/makeDb/trackDb/human/hg38/imprinting.ra @@ -1,90 +1,189 @@ track imprinting shortLabel Imprinting longLabel Genomic imprinting: allele-specific methylation and imprinted regions group regulation superTrack on priority 3.5 track methBaseAsm parent imprinting on shortLabel MethBase2 ASM - longLabel Imprinting: fraction of MethBase2 methylomes with allele-specific methylation at each CpG + longLabel Imprinting - MethBase2: fraction of methylomes with allele-specific methylation at each CpG type bigWig 0 1 bigDataUrl /gbdb/hg38/imprinting/methBaseAsm/hg38.asm.bw visibility full - priority 1 + priority 3 color 85,85,85 autoScale off viewLimits 0:0.5 viewLimitsMax 0:1 maxHeightPixels 100:40:8 alwaysZero on yLineOnOff on yLineMark 0 windowingFunction mean track geneimprint parent imprinting on - shortLabel Geneimprint - longLabel Imprinting: Geneimprint catalog of imprinted and candidate imprinted genes + shortLabel Geneimprint Genes + longLabel Imprinting - Geneimprint: genes curated as imprinted or candidate imprinted type bigBed 9 + bigDataUrl /gbdb/hg38/imprinting/geneimprint/geneimprint.bb visibility pack priority 2 itemRgb on searchIndex name labelFields name,hgncSymbol defaultLabelFields name url https://geneimprint.com/site/genes/Homo_sapiens_$$ urlLabel Geneimprint entry for this gene: urls hgncId="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" mouseOver ${name}
Imprint status: ${status}
Expressed allele: ${expressedAllele}
Band in catalog: ${catalogBand}
Resolved to: ${hgncSymbol} (${resolvedBy}) filterValues.status Imprinted,Predicted,Not Imprinted,Conflicting Data,Provisional Data,Tissue Dependent,Unknown filterType.status multipleListOr filterLabel.status Filter by imprint status filterValues.expressedAllele Paternal,Maternal,Biallelic,Isoform Dependent,Random,Unknown filterType.expressedAllele multipleListOr filterLabel.expressedAllele Filter by expressed allele track akbariIdmr parent imprinting on shortLabel Akbari iDMRs - longLabel Imprinting: imprinted differentially methylated regions compiled from five genome-wide studies + longLabel Imprinting - Akbari et al.: imprinted DMRs compiled from five genome-wide studies type bigBed 9 + bigDataUrl /gbdb/hg38/imprinting/akbari2023/akbariIdmr.bb visibility pack - priority 3 + priority 4 itemRgb on searchIndex name,gene labelFields gene,name defaultLabelFields gene skipEmptyFields on mouseOver ${name}
Methylated allele: ${methylatedAllele}
Evidence: ${evidence}
Reported by: ${studies} filterValues.methylatedAllele Maternal,Paternal filterType.methylatedAllele multipleListOr filterLabel.methylatedAllele Filter by methylated allele filterValues.evidence Multiple studies,Single study filterType.evidence multipleListOr filterLabel.evidence Filter by evidence filterValues.studies Akbari,Court,Hernandez,Joshi,Zink filterType.studies multipleListOr filterLabel.studies Filter by source study track omimImprint parent imprinting on - shortLabel OMIM Imprinted - longLabel Imprinting: genes curated as imprinted by OMIM, from GeneScout + shortLabel OMIM Genes + longLabel Imprinting - OMIM: genes curated as imprinted or candidate imprinted, from GeneScout type bigBed 9 + bigDataUrl /gbdb/hg38/imprinting/omimImprint/omimImprint.bb visibility pack - priority 4 + priority 1 itemRgb on searchIndex name url https://omim.org/entry/$$ urlLabel OMIM entry: urls mimNumber="https://omim.org/entry/$$" skipEmptyFields on mouseOver ${name}
${geneName}
OMIM: ${entryType}
Band: ${cytoLocation} filterValues.entryType OMIM gene,No OMIM entry filterType.entryType multipleListOr filterLabel.entryType Filter by whether OMIM has a gene entry + + track kaplanImprint + parent imprinting on + compositeTrack on + shortLabel ASM Atlas + longLabel Imprinting - ASM Atlas: allele-specific methylation in 39 cell types (Rosenski 2025) + type bigBed 9 + + visibility hide + priority 5 + itemRgb on + skipEmptyFields on + pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19" + + track kaplanParentalAsm + parent kaplanImprint on + shortLabel Parental ASM + longLabel Imprinting - ASM Atlas: regions where the methylation state follows the parent of origin + type bigBed 9 + + bigDataUrl /gbdb/hg38/imprinting/kaplanImprint/kaplanParentalAsm.bb + visibility pack + priority 1 + searchIndex name + labelFields name,icrName + defaultLabelFields name + urls snps="https://www.ncbi.nlm.nih.gov/snp/$$" + mouseOver ${name}
Region: ${regionType}
Type: ${icrType}
Imprinted genes nearby: ${imprintedGenes}
Cell types: ${cellTypeCount}
Methylation in oocyte / sperm: ${methOocyte} / ${methSperm} + filterValues.regionType Known imprinting control region,Novel region near an imprinted gene,Novel region + filterType.regionType multipleListOr + filterLabel.regionType Filter by how the region relates to known imprinting + filterValues.icrType Oocyte gDMR,Sperm gDMR,Secondary DMR,Oocyte gDMR- secondary DMR,Sperm gDMR-secondary DMR,unclear + filterType.icrType multipleListOr + filterLabel.icrType Filter by the gamete the methylation comes from + filterByRange.cellTypeCount on + filter.cellTypeCount 1:73 + filterLimits.cellTypeCount 1:73 + filterLabel.cellTypeCount Number of cell types supporting the region + filterByRange.snpCount on + filter.snpCount 1:39 + filterLimits.snpCount 1:39 + filterLabel.snpCount Number of SNPs used to phase the region + + track kaplanIcr + parent kaplanImprint on + shortLabel ICRs Revised + longLabel Imprinting - ASM Atlas: control regions with boundaries revised from fragment-level methylation + type bigBed 9 + + bigDataUrl /gbdb/hg38/imprinting/kaplanImprint/kaplanIcr.bb + visibility pack + priority 2 + searchIndex name + labelFields name + defaultLabelFields name + mouseOver ${name}
Type: ${icrType}
Associated genes: ${genes}
Recovered as parent-of-origin ASM: ${parentalAsm} + filterValues.icrType Oocyte gDMR,Sperm gDMR,Secondary DMR,Oocyte gDMR- secondary DMR + filterType.icrType multipleListOr + filterLabel.icrType Filter by the gamete the methylation comes from + filterValues.parentalAsm yes,no + filterType.parentalAsm multipleListOr + filterLabel.parentalAsm Filter by whether this study recovered the region + +# track kaplanAsm +# parent kaplanImprint off +# shortLabel SNP-linked ASM +# longLabel Imprinting - ASM Atlas: bimodal regions where methylation follows a heterozygous SNP +# type bigBed 9 + +# bigDataUrl /gbdb/hg38/imprinting/kaplanImprint/kaplanAsm.bb +# visibility dense +# priority 3 +# labelFields name +# defaultLabelFields name +# urls snps="https://www.ncbi.nlm.nih.gov/snp/$$" +# mouseOver ${name}
ASM SNPs: ${snps}
Alleles: ${alleles}
Cell types: ${cellTypeCount}
Best adjusted p: ${minAdjP} +# filterByRange.snpCount on +# filter.snpCount 1:63 +# filterLimits.snpCount 1:63 +# filterLabel.snpCount Number of ASM SNPs in the region +# filterByRange.cellTypeCount on +# filter.cellTypeCount 1:81 +# filterLimits.cellTypeCount 1:81 +# filterLabel.cellTypeCount Number of cell types supporting the region + + track kaplanBimodal + parent kaplanImprint off + shortLabel Bimodal Meth + longLabel Imprinting - ASM Atlas: regions where DNA fragments carry two distinct methylation states + type bigBed 9 + + bigDataUrl /gbdb/hg38/imprinting/kaplanImprint/kaplanBimodal.bb + visibility dense + priority 4 + labelFields name + defaultLabelFields name + mouseOver ${name}
${cellTypes} + filterValues.cellTypes Adipocytes,Bladder-Ep,Blood-B,Blood-Granul,Blood-Mono+Macro,Blood-NK,Blood-T,Bone-Osteob,Breast-Basal-Ep,Breast-Luminal-Ep,Colon-Ep,Colon-Fibro,Dermal-Fibro,Endothel,Epid-Kerat,Eryth-prog,Fallopian-Ep,Gallbladder,Gastric-Ep,Head-Neck-Ep,Heart-Cardio,Heart-Fibro,Kidney-Ep,Liver-Hep,Lung-Ep-Alveo,Lung-Ep-Bron,Neuron,Oligodend,Ovary-Ep,Pancreas-Acinar,Pancreas-Alpha,Pancreas-Beta,Pancreas-Delta,Pancreas-Duct,Prostate-Ep,Skeletal-Musc,Small-Int-Ep,Smooth-Musc,Thyroid-Ep + filterType.cellTypes multipleListOr + filterLabel.cellTypes Filter by cell type + filterByRange.cellTypeCount on + filter.cellTypeCount 1:22 + filterLimits.cellTypeCount 1:22 + filterLabel.cellTypeCount Number of cell types sharing the region