Question: Is it logical to compare the expression FPKM with the percent methylation data at genes?
gravatar for maria2019
11 weeks ago by
maria201990 wrote:


I have methylation data (C frequency from Meth call-bismark) and Bulk RNA-seq FPKM (from RSEM) on a cell line.

I am only interested in comparing RNA-seq and methylation relations at some specific genes on this cell line. ( I do not have any other control cell line - No Foldchange, FDR, etc).

Is it logical just to compare the expression FPKM with the mean percent methylation?

For example, I am interested in genes A, B, C

Reporst that I have:

               A    B   C

Methylation:  100   80  60

Expression:   300  40   250

-> Scores for each gene:

gene A: 300/100 = 3

gene B: 40/80 = ./5

gene C: 250/60= 4.16

Will this be a right comparison/scoring?

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by maria201990

Depends on your question. Ff you want to check if gene methylation (gene body methylation) is correlated to its expression, then one might try to see if there is indeed a linear correlation between gene body methylation and expression. I did not follow the methylation field in the last years but I think there is indeed a connection, so I suggest to scan the literature for it. Let some papers inspire you about potential analysis strategies and ways to visualize this.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by ATpoint31k

Thanks for your comment. I have been reading different articles. There is for example an article (doi:10.1038/nature18606) that compares FPKM (log2) and Normalized RPKM (ATAC-seq data) - Figure 2a.

I am trying to find if anyone has done this based on methylation and how accurate it would be. Since for methylation I only have CpGs and I calculate the mean of CpG methylations at genes. I am not sure if that would be a fair comparison.

ADD REPLYlink written 11 weeks ago by maria201990
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