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/omimImprint.html src/hg/makeDb/trackDb/human/hg38/omimImprint.html index 700c683f7f2..f7715271866 100644 --- src/hg/makeDb/trackDb/human/hg38/omimImprint.html +++ src/hg/makeDb/trackDb/human/hg38/omimImprint.html @@ -1,148 +1,152 @@ <h2>Description</h2> <p> -This track shows the genes that OMIM, the catalog of human genes and genetic -disorders curated at Johns Hopkins, marks as imprinted. The OMIM staff assign -that mark by reading the primary literature. It is published only through +Part of the <a href="hgTrackUi?db=$db&hgsid=${hgsid}&g=$parentTrack">Imprinting</a> track collection, this track shows the genes that OMIM, the catalog of +human genes and genetic disorders curated at Johns Hopkins, marks as imprinted or candidate +imprinted. The OMIM staff assign that mark by reading the primary literature. It is published only through <a href="https://genescout.omim.org/" target="_blank">GeneScout</a>, OMIM's tool for listing the genes and phenotypes inside a set of genomic intervals, which appends <tt>(I)</tt> to the coordinates of a flagged gene in its Location column. The mark is not part of the OMIM gene map and does not appear in any of -the OMIM download files. Because the set is curated by hand it is smaller and -more conservative than the computational predictions in the other tracks of -this collection, and it is tied directly to the OMIM entries for each gene. +the OMIM download files. Because the set is curated by hand it is smaller than +the computational predictions in the other tracks of this collection, and it is +tied directly to the OMIM entries for each gene. +</p> + +<p> +The OMIM curators point out that the flag covers both genes where imprinting is +established and genes where it is still only a candidate, and that the export +does not say which is which. A gene in this track is therefore a pointer into +its OMIM entry rather than a settled call. </p> <p> The track holds 459 loci. Of these, 225 have an OMIM gene entry of their own and 234 appear in the gene map without one; the second group is mostly antisense transcripts, long non-coding RNAs and microRNAs sitting inside imprinted clusters, such as KCNQ1-AS1 and INS-IGF2. </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> Each item is one OMIM gene entry, drawn over the gene span that OMIM gives. OMIM does not report a strand, so the items are drawn without one. Clicking an item opens a page with the MIM number, the full gene name, the other symbols OMIM lists for the locus, and every OMIM phenotype associated with the gene. The gene symbol links to the OMIM entry. </p> <p> -OMIM records that a gene is imprinted but not which parental copy is active, so +OMIM records that a gene is imprinted or a candidate, but not which parental copy is active, so every item here is drawn in the neutral gray that this collection uses for annotations without a parent of origin. Vermillion and blue keep their meaning on the other subtracks: the maternal and the paternal copy. </p> <table class="stdTbl"> <tr><th style="background-color:#555555;width:2em"> </th> - <td>Gray — imprinted according to OMIM, parental copy not stated</td></tr> + <td>Gray — imprinted or candidate imprinted according to OMIM, parental copy + not stated</td></tr> </table> <p> Methylation itself is annotated elsewhere. The Kaplan lab human methylation atlas is a separate track, <a href="hgTrackUi?g=humanMethylationAtlasSummary">Human Methylation Atlas Summary</a>, under DNA Methylation. </p> <p> A filter separates the genes that have an OMIM gene entry of their own from the loci that appear in the gene map without one, which are mostly antisense transcripts and other non-coding genes at imprinted clusters. It does not filter anything out by default. </p> <h2>Methods</h2> <p> OMIM curators read the primary literature and record, for each gene, the phenotypes it causes, the mode of inheritance and a set of annotations, one of -which is that the gene is imprinted. That annotation surfaces only in GeneScout +which is that the gene is imprinted or a candidate for it. That annotation surfaces only in GeneScout output, where it is appended as <tt>(I)</tt> to the coordinates in the Location column; it is in neither the OMIM gene map nor the OMIM download files. GeneScout is described in Applegate et al. (2022). </p> <p> The gene list was exported from <a href="https://genescout.omim.org/" target="_blank">GeneScout</a> as a tab-delimited file, using a search that covers every chromosome on assembly GRCh38, and the flagged entries were converted to browser coordinates. GeneScout also lists OMIM phenotype entries alongside genes; those are mapped disease regions rather than gene positions, some of them tens of megabases long, so they are not shown here. The Genome Browser already has them in the <a href="hgTrackUi?g=omimLocation">OMIM Cyto Loci</a> track. The processing steps 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> and the script is in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/imprinting" target="_blank">makeDb/scripts/imprinting</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>omimImprint</i>. </p> <p> For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/omimImprint/" target="_blank">our download server</a>. The file for this track is called <tt>omimImprint.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain features within a given range, e.g. <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/omimImprint/omimImprint.bb -chrom=chr15 -start=23000000 -end=26000000 stdout</tt> </p> <p> The original gene list can be exported from <a href="https://genescout.omim.org/" target="_blank">GeneScout</a>. Use of OMIM resources requires agreement to the <a href="https://omim.org/help/agreement" target="_blank">OMIM terms of use</a>. </p> <h2>Credits</h2> <p> Thanks to the OMIM curators at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, for maintaining the catalog, and in particular to Joanna Amberger for explaining how to export the gene list from GeneScout. </p> <h2>References</h2> <p> Applegate CD, Schiettecatte F, Hamosh A, Amberger JS. <a href="https://doi.org/10.1002/cpz1.530" target="_blank"> Exploring Genes and Phenotypes Within Chromosomal Regions Using OMIM's GeneScout</a>. <em>Curr Protoc</em>. 2022 Sep;2(9):e530. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36130039" target="_blank">36130039</a> </p> <p> Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25428349" target="_blank"> OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders</a>. <em>Nucleic Acids Res</em>. 2015 Jan;43(Database issue):D789-98. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25428349" target="_blank">25428349</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383985/" target="_blank">PMC4383985</a> </p>