This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to select one gene at a CpG site?

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

gene assembly
• 2,112 views • link
updated by wuhan9281 • wuhan9281 • written by hansong798 • hansong798

Please provide an example site and the genes you see.

• 1 views • link
written by GenoMax GenoMax

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

• 1 views • link
written by hansong798 • hansong798

Hi! I am also puzzled with this problem. How did you deal with this problem at last?

• 0 views • link
written by wuhan9281 • wuhan9281

1 answer

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).

• 1 views • link
written by Charles Warden Charles Warden

Log in to answer this question.

More posts like this