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

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

dna methylation hyper-hypomethyaltion same gene
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written by nazaninhoseinkhan nazaninhoseinkhan

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.

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written by Jan Oosting Jan Oosting

Thanks Jan.

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

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written by nazaninhoseinkhan nazaninhoseinkhan

I could find the annotation file from UCSC table browser

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written by nazaninhoseinkhan nazaninhoseinkhan

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