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/methBaseAsm.html src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html index b137fc818a7..7c86132d86f 100644 --- src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html +++ src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html @@ -1,50 +1,47 @@ <h2>Description</h2> <p> -Most genes are expressed from both the maternal and the paternal copy of a -chromosome. A small number of genes break this rule: they are -<em>imprinted</em>, meaning that only the copy inherited from one parent is -active while the other copy is silenced. The mark that keeps the two copies -apart is DNA methylation. At an imprinted locus, one allele carries methylated -CpG sites and the other does not, a pattern called allele-specific methylation -(ASM). Regions with this pattern are candidates for imprinting control regions, -the switches that set the expression of whole gene clusters. +This track summarizes allele-specific methylation (ASM) across thousands of human methylomes. At an imprinted locus one allele carries methylated CpG sites and the other does not, so a region that shows this pattern in many independent samples is a candidate imprinting control region. </p> <p> Whole-genome bisulfite sequencing reads are long enough to cover several CpG sites at once, so the methylation states of neighboring sites on the same DNA molecule can be read together. When the reads at a locus fall into two clearly separated groups, one mostly methylated and one mostly unmethylated, that locus shows allele-specific methylation. This track shows, for every CpG site in the genome, the fraction of MethBase2 human methylomes in which the site was called part of an allelically methylated region (AMR). Values range from 0 to 1. High values mean that many independent samples show two differently methylated alleles at that site, which is the expected signature of a constitutive imprinted region. Lower but non-zero values point at loci where allele-specific methylation is restricted to certain tissues or is driven by sequence variation rather than by imprinting. </p> <p> The score is a summary across samples, not a measurement in any single sample. A value of 0.5 does not mean that half of the DNA molecules are methylated; it means that about half of the surveyed methylomes had an AMR call covering that CpG. </p> +<p> +See the <a href="hgTrackUi?g=imprinting">Imprinting</a> track collection page for background on genomic imprinting and for the color scheme shared by all of its subtracks. +</p> + <h2>Display Conventions and Configuration</h2> <p> The track is a signal graph with one value per CpG site. The default vertical range is 0 to 0.5, since even the strongest known imprinted regions rarely exceed that fraction across a set of samples this diverse. The range, the graph height, the smoothing window and the aggregation function can all be changed on the track configuration page. Positions between CpG sites carry no data and are drawn as gaps. </p> <p> The per-sample methylation levels, hypomethylated regions and read coverage that this summary is derived from are published by the Smith lab as a track hub, which can be loaded from @@ -71,33 +68,32 @@ methylation state and one in which the two alleles have separate states. The window is called an AMR when the two-allele model fits significantly better, using a likelihood ratio test with a false discovery rate correction; windows need at least 4x mean coverage per CpG to be tested, and neighboring AMRs closer than 1 kb are merged. The statistical model is described in Fang et al. (2012). The score shown here is the number of methylomes whose AMR set covers a given CpG, divided by the number of methylomes tested. </p> <p> The data file was downloaded from <a href="http://smithlab.usc.edu/methbase/data/common/hg38/hg38.asm.bw" target="_blank">http://smithlab.usc.edu/methbase/data/common/hg38/hg38.asm.bw</a>, the "common" section of the MethBase2 track hub at <a href="http://smithlab.usc.edu/trackdata/methylation/hub.txt" target="_blank">http://smithlab.usc.edu/trackdata/methylation/hub.txt</a>. The file is a bigWig and was used as it is, without reformatting or -recalculation; it covers 29,401,795 CpG positions on the 25 main chromosomes -(chr1 to chr22, chrX, chrY, chrM) and no positions were dropped. The steps we -ran are documented in the +recalculation. It carries a value at each of 29,401,795 CpG positions, on +chr1 to chr22, chrX, chrY and chrM. The steps we ran are documented in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/imprinting.txt" target="_blank">imprinting makeDoc</a>. </p> <h2>Data Access</h2> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>methBaseAsm</i>. </p> <p> For automated download and analysis, the annotation is stored in a bigWig file