+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 +GeneScout, OMIM's tool +for listing the genes and phenotypes inside a set of genomic intervals, which +appends (I) 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 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. +
+ ++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 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. +
+ ++OMIM records that a gene is imprinted 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. +
+ +| + | Gray — imprinted according to OMIM, parental copy not stated |
|---|
+Methylation itself is annotated elsewhere. The Kaplan lab human methylation +atlas is a separate track, +Human Methylation Atlas +Summary, under DNA Methylation. +
+ ++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. +
+ ++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 +output, where it is appended as (I) 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). +
+ ++The gene list was exported from +GeneScout 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 +OMIM Cyto Loci track. The processing +steps are documented in the +imprinting makeDoc +and the script is in +makeDb/scripts/imprinting. +
+ ++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=omimImprint. +
+ ++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 omimImprint.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/omimImprint/omimImprint.bb -chrom=chr15 -start=23000000 -end=26000000 stdout +
+ ++The original gene list can be exported from +GeneScout. Use of OMIM +resources requires agreement to the +OMIM terms of use. +
+ ++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. +
+ ++Applegate CD, Schiettecatte F, Hamosh A, Amberger JS. + +Exploring Genes and Phenotypes Within Chromosomal Regions Using OMIM's GeneScout. +Curr Protoc. 2022 Sep;2(9):e530. +PMID: 36130039 +
+ ++Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. + +OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic +disorders. +Nucleic Acids Res. 2015 Jan;43(Database issue):D789-98. +PMID: 25428349; PMC: PMC4383985 +
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