22fc293ddc00fce956d75fbcdb237e5d19d08fd5
max
  Thu Sep 3 14:39:29 2026 -0700
Three more Imprinting subtracks on hg38: Geneimprint, Akbari iDMRs, OMIM

Geneimprint: the human catalog of imprinted and candidate imprinted genes
from geneimprint.com, 274 genes. The catalog gives only a cytogenetic band,
so symbols are resolved against the HGNC track, with fallbacks for small RNA
clusters and for symbols HGNC has retired.

Akbari iDMRs: the 192 imprinted differentially methylated regions that Akbari
et al. 2023 (PMID 36777186) compiled from five genome-wide studies. Their
published coordinates are 1-based inclusive, not bed, as their own PatMat
reader shows, so the starts are shifted.

OMIM: the 459 loci that OMIM curates as imprinted. That call is published only
through GeneScout and is in no OMIM download file, so the input is a GeneScout
export made by hand from a browser. OMIM phenotype entries, which are mapped
disease regions up to 90 Mb rather than gene positions, are left out.

Also unifies the color scheme across the collection, so vermillion always means
the maternal copy, blue the paternal copy and gray no parent of origin, and
relates the collection to the Human Methylation Atlas.

refs #37599

diff --git src/hg/makeDb/trackDb/human/hg38/imprinting.ra src/hg/makeDb/trackDb/human/hg38/imprinting.ra
index be33989607a..94a70e856f0 100644
--- src/hg/makeDb/trackDb/human/hg38/imprinting.ra
+++ src/hg/makeDb/trackDb/human/hg38/imprinting.ra
@@ -1,25 +1,90 @@
 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
     type bigWig 0 1
     bigDataUrl /gbdb/hg38/imprinting/methBaseAsm/hg38.asm.bw
     visibility full
     priority 1
-    color 255,64,64
+    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
-    dataVersion MethBase2 hg38 ASM, 2025-07-14
+
+    track geneimprint
+    parent imprinting on
+    shortLabel Geneimprint
+    longLabel Imprinting: Geneimprint catalog of imprinted and candidate imprinted genes
+    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 <b>${name}</b><br><b>Imprint status</b>: ${status}<br><b>Expressed allele</b>: ${expressedAllele}<br><b>Band in catalog</b>: ${catalogBand}<br><b>Resolved to</b>: ${hgncSymbol} (${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
+    type bigBed 9 +
+    bigDataUrl /gbdb/hg38/imprinting/akbari2023/akbariIdmr.bb
+    visibility pack
+    priority 3
+    itemRgb on
+    searchIndex name,gene
+    labelFields gene,name
+    defaultLabelFields gene
+    skipEmptyFields on
+    mouseOver <b>${name}</b><br><b>Methylated allele</b>: ${methylatedAllele}<br><b>Evidence</b>: ${evidence}<br><b>Reported by</b>: ${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
+    type bigBed 9 +
+    bigDataUrl /gbdb/hg38/imprinting/omimImprint/omimImprint.bb
+    visibility pack
+    priority 4
+    itemRgb on
+    searchIndex name
+    url https://omim.org/entry/$$
+    urlLabel OMIM entry:
+    urls mimNumber="https://omim.org/entry/$$"
+    skipEmptyFields on
+    mouseOver <b>${name}</b><br>${geneName}<br><b>OMIM</b>: ${entryType}<br><b>Band</b>: ${cytoLocation}
+    filterValues.entryType OMIM gene,No OMIM entry
+    filterType.entryType multipleListOr
+    filterLabel.entryType Filter by whether OMIM has a gene entry