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/geneimprint.html src/hg/makeDb/trackDb/human/hg38/geneimprint.html index 3f85a63ec2c..fc7a1399f79 100644 --- src/hg/makeDb/trackDb/human/hg38/geneimprint.html +++ src/hg/makeDb/trackDb/human/hg38/geneimprint.html @@ -1,148 +1,144 @@ <h2>Description</h2> <p> -This track shows the human part of the Geneimprint catalog, with each gene -placed on the genome. The catalog itself gives only a cytogenetic band, so the +Part of the <a href="hgTrackUi?db=$db&hgsid=${hgsid}&g=$parentTrack">Imprinting</a> track collection, this track shows the human part of the Geneimprint +catalog, with each gene placed on the genome. The catalog itself gives only a cytogenetic band, so the coordinates here come from resolving the gene symbols against the <a href="hgTrackUi?g=hgnc">HGNC</a> gene annotation. Note that the track contains all of the catalog, including 18 genes that Geneimprint records as <em>not</em> imprinted and 10 whose status is unknown. Use the filters on the track configuration page to narrow the display to the evidence levels you want. </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 gene from the catalog, drawn over the span of the resolved locus. The item is labeled with the name Geneimprint uses, which for older entries can differ from today's approved symbol; the configuration page can switch the label to the approved symbol instead. Clicking an item opens a page with the imprint status, the expressed allele, the band the catalog gives, and links to the Geneimprint and HGNC entries. </p> <p> The color shows which parental copy is expressed: </p> <table class="stdTbl"> <tr><th style="background-color:#0072B2;width:2em"> </th> <td>Paternal — the copy inherited from the father is expressed, so the maternal copy is silenced</td></tr> <tr><th style="background-color:#D55E00;width:2em"> </th> <td>Maternal — the copy inherited from the mother is expressed, so the paternal copy is silenced</td></tr> <tr><th style="background-color:#009E73;width:2em"> </th> <td>Biallelic — both copies are expressed, the gene was tested and is not imprinted</td></tr> <tr><th style="background-color:#E69F00;width:2em"> </th> <td>Isoform dependent — some transcripts of the gene are imprinted and others are not</td></tr> <tr><th style="background-color:#CC79A7;width:2em"> </th> <td>Random — one copy is silenced, but which one is not decided by the parent of origin</td></tr> <tr><th style="background-color:#555555;width:2em"> </th> <td>Unknown — the expressed copy has not been determined</td></tr> </table> <p> Vermillion, blue and gray mean the same thing on every subtrack of this collection; the three colors above them are used only by this catalog. </p> <p> Two filters are available, one on imprint status and one on expressed allele. Neither filters anything out by default. </p> <h2>Methods</h2> <p> Geneimprint is curated by hand from the imprinting literature and is maintained by Randy L. Jirtle. A large share of the entries marked as predicted rather than confirmed comes from the genome-wide machine learning screen of Luedi et al. (2007), which scored every human gene on the sequence features that distinguish known imprinted genes, mainly the arrangement of repeats and transcription factor binding sites around the locus. The catalog records for each gene the expressed parental allele and an evidence level: imprinted, not imprinted, predicted, conflicting data, provisional data, tissue dependent or unknown. The site does not publish a definition of these levels. </p> <p> The catalog table was downloaded from <a href="https://geneimprint.com/site/genes-by-species.Homo+sapiens" target="_blank">https://geneimprint.com/site/genes-by-species.Homo+sapiens</a> and parsed out of the HTML page. Geneimprint gives a cytogenetic band but no coordinates, so each gene symbol was resolved against the HGNC track, trying in turn the approved symbol, the previous approved symbols and the alias symbols, first for the catalog name and then for each of the aliases the catalog lists. Only the main chromosomes were considered, so an alternate haplotype can never win a match. Where a symbol matched more than one locus, the one whose cytogenetic band agreed with the catalog was taken. Two cluster names, SNORD115@ and SNORD116, do not exist as single loci and were spanned from the first to the last numbered member of their family. One symbol that HGNC has retired, PRR25, was resolved through RefSeq instead. 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> <p> The catalog lists 281 entries and 274 of them are shown. Four could not be placed because their gene identifiers have been retired and no longer match any locus; one of those, PWCR1, is an older name for the SNORD116 cluster, which is in the track under that name. Three more genes appear twice in the catalog under an old and a current symbol, and each pair is drawn once, carrying both names. </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>geneimprint</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/geneimprint/" target="_blank">our download server</a>. The file for this track is called <tt>geneimprint.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/geneimprint/geneimprint.bb -chrom=chr15 -start=23000000 -end=26000000 stdout</tt> </p> <p> The original catalog can be browsed at <a href="https://geneimprint.com/site/genes-by-species.Homo+sapiens" target="_blank">https://geneimprint.com/site/genes-by-species.Homo+sapiens</a>. </p> <h2>Credits</h2> <p> Thanks to Randy L. Jirtle for curating and publishing the Geneimprint catalog. </p> <h2>References</h2> <p> Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ. <a href="https://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=18055845" target="_blank"> Computational and experimental identification of novel human imprinted genes</a>. <em>Genome Res</em>. 2007 Dec;17(12):1723-30. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18055845" target="_blank">18055845</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099581/" target="_blank">PMC2099581</a> </p>