What should I do when some probes of a gene is detected as hypomethylated and other probes of the same gene is hypermethylated

Question

[nazaninhoseinkhan]

Dear all,

I have carried out differential methylation analysis on TCGA data.

Strangely I have found 13 genes detected as hypermethylated and hypomethylated at the same time. Different probes for the same genes show this discrepancy.

My question is that should I remove these 13 genes from rest of my study?

Have you ever been faced with the same issue?

Looking forward your guides

Nazanin

[Jan Oosting]

You should probably look at the functional domains at which the probes are located. Pretty much all probes that are not close to the promoter region of a gene are usually methylated.

I find it helps to visualize the location, and extent of methylation relative to the exons (and especially the first exon) of a gene.

[nazaninhoseinkhan]

Thanks Jan.

Can u guide me how to find the probe annotation file for Illumina human methylation 450 array?

[nazaninhoseinkhan]

I could find the annotation file from UCSC table browser