As in the title.
I got the methylation status of several genes in different cell lines by bisulfite sequencing.
More specifically, I have the sequencing data from the amplicons of these genes with different percentages of methylation on each nucleotide.
However, I am not sure which statistical or other methods I shall use to compare and interpret them.
Please help me with it.
With sincere thanks.
Hi,
First, you need to quantify and to filter DNA-methylated sites by using PM value, which means the percentage of molecules that were methylated. Then, you need to correlate the PM values between these genes according to their CpG sites and merged them into one dataset. After, use the mean PM value of each CpG site in different genes as the final PM value.
If you want also to quantify the expression level of each gene you must use the RPKM (reads per kilobase of transcript per million reads) values.
You can perform this by using the ‘WGCNA’ R package which only works with R version 3.0.0 and higher.
Link for the package: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/
Hope this may help you.
Walid Hassene Hamri
Dear Walid, thank you very much for your answer.
I already have the exact percentage of each CpG in these genes.
Just don't know which parameter is the best to make the comparison.
For example, let's assume there are 5 CpG in my amplicon and two samples.
The methylation percentage of sample A is 50/0/50/0/50.
The methylation percentage of sample B is 100/0/0/0/50.
If I get it right, you suggest using the mean value, which is the same here.
But can I say they have no difference in methylation status?
Best regards and thank you again.
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