Question: How to select one gene at a CpG site?
0
gravatar for hansong798
4 months ago by
hansong79820
hansong79820 wrote:

Hello, I have some problem to process TCGA public data.

I downloaded TCGA breast cancer's methylation data with annotation information using "TCGAbiolinks" package of R but there are some CpG sites which have multiple gene symbols at each.

However, I need data which have 1 gene symbol at 1 CpG site for analysis.

Is there any criteria or method?

enter image description here

assembly gene • 208 views
ADD COMMENTlink modified 4 months ago by Charles Warden6.6k • written 4 months ago by hansong79820

Please provide an example site and the genes you see.

ADD REPLYlink written 4 months ago by genomax65k

I added figure. It is a part of my annotation data.

ADD REPLYlink written 4 months ago by hansong79820
0
gravatar for Charles Warden
4 months ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

I think bi-directional promoters exist for a non-trivial number of genes.

While I don't think the overall percentage (or the gene-overlapping percentage) is as high as you may expect from your screenshot, one possible solution would be to use the gene regions like TSS200 or TSS1500 and only consider them if they only have one gene annotation (and/or keep the paired name, and visualize methylation and/or expression for the region including both genes).

ADD COMMENTlink written 4 months ago by Charles Warden6.6k
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