If you know what genes you are interested in, then do a methylation analysis directly.  qMSP is one type of assay.  If you do not know what genes might be getting methylated, you could use the Illumina Infinium 850K beadarray method.

Illumina- Infinitum-27 Blead -Chips

Dear Dr. Adam

I read that the larg T antigen of polyoma viruses interact and interfere with the function of P53 and Rb (protein - protein interaction) also it hyperactivate the DNMT1 and DNMT2B which they hypermethylate a lot of tumor suppressor genes including p53 and Rb (so it might not be properly expressed), I want to study the level of methylation especially for p53 and Rb as well as a lot of cell cycle regulators including (P15, P16, P21, and P27) I understood that Illumina Infinium 850K beadarray method could serve this goals. but what about the protein -protein interaction between the larg T antigen and P53 / Rb, is it better to study it using a bioinformatics tools or how can I study it in the wet lab. 

please support me with your opinion.

thank you for your generous help 

Hello

I agree with Adam Karpf · 

See link here hope help you 

Good Luck 

http://www.sciencedirect.com/science/article/pii/S2311300616300209

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151012/