Part of the Imprinting track collection, this track shows 50 imprinted differentially methylated regions (DMRs) that Monk et al. proposed as the standard set for diagnostic testing of imprinting disorders. Each region has a systematic name built from the gene, the position relative to it (promoter, exon, intron or intergenic) and the type of region, for example H19/IGF2:IG-DMR. The older names under which a region is commonly known, such as ICR1 or KvDMR1, are listed as aliases.
For each region the track gives the parent whose allele carries the methylation, the number of CpG sites, whether the methylation is established in the oocyte or in the sperm (germline DMR) or is acquired later and depends on a neighboring germline DMR (secondary DMR), and the matching Locus Reference Genomic (LRG) record where one exists. The coordinates in the paper are in hg19. Everything here was lifted to hg38, and all 50 regions lifted without loss.
Regions are colored by the parent whose allele is methylated:
| Red: the maternal allele is methylated | |
| Blue: the paternal allele is methylated |
The track can be filtered by methylated allele and by germline origin. The details page shows all columns of the original table and the position as published in hg19.
Monk et al. defined the extent of each DMR from methyl-seq data sets and named the regions with the nomenclature proposed by EUCID, using HGNC-approved gene names, so that the same region is reported under one name in the clinic. See the paper for details.
The table was copied from Table 1 of the paper on the PubMed Central web page. Starts in the table are 1-based, so one was subtracted to get the BED start. The BED file was lifted from hg19 to hg38 with liftOver and the hg19-to-hg38 chain file. All 50 regions were converted and none was lost. The thousands separators the web page inserted into the LRG identifiers were removed, the dash and prime characters in two names were converted to ASCII, and M and P were spelled out as Maternal and Paternal. The coordinates of the region SNRPN:Int1-DMR1 are shown as published, 100 kb long for 44 CpGs, which is probably a typing error in the paper. See the makeDoc file and the scripts.
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=monk2018Imprint.
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 monk2018Imprint.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/monk2018/monk2018Imprint.bb -chrom=chr21 -start=0 -end=100000000 stdout
The original annotation source data can be downloaded from Table 1 of the paper.
Monk D, Morales J, den Dunnen JT, Russo S, Court F, Prawitt D, Eggermann T, Beygo J, Buiting K, Tümer Z et al. Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains. Epigenetics. 2018;13(2):117-121. PMID: 27911167; PMC: PMC5873357