I'm trying to find GC methylation percent of a specific gene promoter in mouse ESCs, I found http://imethyl.iwate-megabank.org and http://www.methdb.net websites as available databases, however, after putting my favorite gene ID number I was unable to interpret all peaks shown in those website, I was wondering if anybody knows how can I interpret and present those information? OR is there any other way to find methylation status of a gene? Thanks,
Generally speakingly, the epigenetic landscape towards specific genes has two dimension: DNA methylation and histone modification. As for GC methylation percent, I think you should find some DNA methylation profiles rather than histone marks. Through DNA hypermethylation at the promoter regions together with high level of H3K27me3 modification, however, there are still some different patterns in some situations from recent researches. So I don't think you should have some useful information from histone marks.
Let's come back to your original question.
Firstly, I have checked your supplied websites in your questions, and you can't even get any useful information as you want. Because the cell lines were not the mES cell lines, their DNA methylation patterns wouldn't be the same to some degree. In my opinion, you could find some papers about DNA methylation profiles from mESCs, such as WGBS datasets from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5653840.
Wish you good luck!
Hi Azin
you can also go to the UCSC web server and apply the right parameters (species/genome/genename) and look on the genome browser what's up with the right options.
UCSC (http://genome.ucsc.edu) provides additional tools that could also be interesting in your research, take some times to get used.
keep safe
fred
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