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/scripts/imprinting/akbariIdmr.as src/hg/makeDb/scripts/imprinting/akbariIdmr.as
new file mode 100644
index 00000000000..27443d11245
--- /dev/null
+++ src/hg/makeDb/scripts/imprinting/akbariIdmr.as
@@ -0,0 +1,24 @@
+table akbariIdmr
+"Imprinted differentially methylated regions compiled by Akbari et al. 2023"
+    (
+    string chrom;                 "Chromosome (or contig, scaffold, etc.)"
+    uint   chromStart;            "Start position in chromosome"
+    uint   chromEnd;              "End position in chromosome"
+    string name;                  "Genes at or near the region"
+    uint   score;                 "Score (unused, always 0)"
+    char[1] strand;               "Strand, not applicable, always ."
+    uint   thickStart;            "Start of thick display"
+    uint   thickEnd;              "End of thick display"
+    uint   reserved;              "Color, set from the methylated allele"
+    string methylatedAllele;      "Methylated Allele|Parental copy that carries the methylation, so the silenced one"
+    string gene;                  "First Gene|First gene listed for this region, used as the short label"
+    string studies;               "Source Studies|Earlier genome-wide studies that reported this region"
+    uint   studyCount;            "Number of Studies|How many of the five source studies reported this region"
+    string evidence;              "Evidence|Reported by several studies, or by one study and confirmed against public methylomes"
+    string indivExamined;         "Individuals Examined|Blood methylomes in which the region could be tested"
+    string indivPartialMeth;      "Individuals Partially Methylated|Of those, how many showed partial methylation"
+    string pctIndivPartialMeth;   "Percent Individuals|Percent of testable individuals with partial methylation"
+    string tissuesExamined;       "Tissues Examined|Tissue methylomes in which the region could be tested"
+    string tissuesPartialMeth;    "Tissues Partially Methylated|Of those, how many showed partial methylation"
+    string pctTissuesPartialMeth; "Percent Tissues|Percent of testable tissues with partial methylation"
+    )