+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 +HGNC gene annotation. Note that the track +contains all of the catalog, including 18 genes that Geneimprint records as +not 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. +
+ ++See the Imprinting track collection page for background on genomic imprinting and for the color scheme shared by all of its subtracks. +
+ ++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. +
+ ++The color shows which parental copy is expressed: +
+ +| + | Paternal — the copy inherited from the father is expressed, + so the maternal copy is silenced |
|---|---|
| + | Maternal — the copy inherited from the mother is expressed, + so the paternal copy is silenced |
| + | Biallelic — both copies are expressed, the gene was tested and + is not imprinted |
| + | Isoform dependent — some transcripts of the gene are imprinted + and others are not |
| + | Random — one copy is silenced, but which one is not decided by + the parent of origin |
| + | Unknown — the expressed copy has not been determined |
+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. +
+ ++Two filters are available, one on imprint status and one on expressed allele. +Neither filters anything out by default. +
+ ++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. +
+ ++The catalog table was downloaded from +https://geneimprint.com/site/genes-by-species.Homo+sapiens +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 +imprinting makeDoc +and the script is in +makeDb/scripts/imprinting. +
+ ++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. +
+ ++The data can be explored interactively in table format with the +Table Browser or the +Data Integrator and exported from there to +spreadsheet or tab-sep tables. From scripts, the data can be accessed through +our API, track=geneimprint. +
+ ++For automated download and analysis, the genome annotation is stored in a +bigBed file that can be downloaded from +our download server. +The file for this track is called geneimprint.bb. Individual regions or +the whole genome annotation can be obtained using our tool +bigBedToBed, 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 +here. +The tool can also be used to obtain features within a given range, e.g. +bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/geneimprint/geneimprint.bb -chrom=chr15 -start=23000000 -end=26000000 stdout +
+ ++The original catalog can be browsed at +https://geneimprint.com/site/genes-by-species.Homo+sapiens. +
+ ++Thanks to Randy L. Jirtle for curating and publishing the Geneimprint catalog. +
+ ++Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ. + +Computational and experimental identification of novel human imprinted genes. +Genome Res. 2007 Dec;17(12):1723-30. +PMID: 18055845; PMC: PMC2099581 +
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