TCGA DATA mRNA and Methylation Genes

Question

[vrrani]

I would like to know the biological significance of common genes of both mRNA and methylation.

For example, of breast cancer data, out of gene-gene network created using methylation features, one can select top '100' genes, similarly, from mRNA gene-gene network if we had selected top '100' genes. Let, the common gene symbols of both mRNA and methylation is 10.

What is these 10 gene symbols biological significance? How to verify their significance?

Thanks & Regards, Reddy Rani V.

[Kevin Blighe]

Where did you see this method of selecting genes?

[vrrani]

The TCGA methylation and mRNA genes of a Breast cancer. When I checked with gene symbols I noticed common genes. For example : ABL1 AKT1 APC AXIN1 CASP8 CDH11 CDK6 CREB1 CTNNB1 DDB2

My question is, Is it a correct study to collect common genes of methylation and mRNA. What is the biological significance of this? If I have to validate these genes, how should I do that?

Thanks & Regards, Reddy Rani V.

[Kevin Blighe]

Well, with methylation and mRNA data, you could check to see if increased methylation resulted in reduced expression of the gene (and vice-versa).

[vrrani]

Hi,

Thanks for your reply.

Why is that inverse relationship? What biological phenomena will allow us to notice this? Can I get any reference for this?

Regards, Reddy Rani V.

[Kevin Blighe]

Hello, there is plenty of literature to support this. Just go to a search engine and use the keywords: ncbi methylation silence gene expression

One of the most well-known mechanisms is female chromosome X (chrX) inactivation by the Xist non-coding RNA. This process silences gene expression from 1 female chrX through methylation (but not completely, and some genes can 'escape' chrX inactivation).