Differentially methylated cytosines (DMCs)

[How to cite NGSmethDB]

Following with the previous example, we will retrieve a list of differentially methylated cytosines (DMCs) between two samples (adipose and adrenal gland) in the gene AMH of the individual STL002.

1. Go to NGSmethDB and follow the path Data access -> Track hubs -> Differential methylation (DMCs) ->  Human – hg38 -> Genome map of DMCs at UCSC.
2. Once at UCSC, type AMH on the search text field, then select ‘AMH (Homo sapiens anti-Mullerian hormone (AMH), mRNA. (from RefSeq NM_000479))’ and finally click go.

3. The browser then will show the genome region of chromosome 19 where the AMH gene is located: chr19:2,249,311-2,252,073.

4. Click Tools -> Table Browser
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5. In group choose ‘NGSmethDB: Differentially methylated cytosines (DMCs)’ and in table choose the sample ‘adipose_adrenalGland_STL002’
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6. In region mark ‘position’ and ensure you have selected the coordinates chr19:2249311-2252073.
7. Click get output to obtain the result table in your browser:

DMCs_AMH

8. If you want to retrieve data for the entire chromosome, go back to the Table Browser page and in region -> position type ‘chr2’ (or whatever else chromosome number you want). To get data for the entire genome, in region click on the button ‘genome’.
9. If you want to save the numerical data to your hard disk, go back to the Table Browser page and then provide a filename in the output file text field.
10. Finally, if you want to send your numerical data to the Galaxy platform for further downstream analyses, go back to the Table Browser page and then tick on Send output to Galaxy.