Question: How to transform DNA Methylation data in TCGA to effect of methylation on gene expression
gravatar for Wayne Lee
22 months ago by
Wayne Lee10
Wayne Lee10 wrote:

Hello everyone!

DNA methylation data in TCGA describe the methylation extent of single site and corresponding effected genes, but I want to transform it to extent of specific gene effected by all of methylation site. For instance, there have one gene and it could be regulate by 5 methylation sites corresponding to 5 rows in the original data, how to integrate them and calculate a single value to describe this gene's expression effected by methylation? If there have any method or tool to do this job?

Thanks a lot! Wayne

tcga dna mathylation • 1.2k views
ADD COMMENTlink modified 22 months ago by Kevin Blighe61k • written 22 months ago by Wayne Lee10
gravatar for Kevin Blighe
22 months ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

Hey Wayne,

What you are aiming to do is... it's an issue in methylatioin studies that is not really discussed or even performed (although I am sure that some Smart Alec reading my answer will go out and trawl the WWW to find some website or 'publication'' where it is very much discussed). The reason is that, unlike gene expression studies where it makes sense to summarise, for example, probe values to gene level, it does not quite make sense when it comes to methylation.

Methylation at different parts of the gene (in genomic co-ordinates) could have very different effects on the resulting transcription of the gene. So, whilst they may each regulate the gene, they do so in different ways. Some of the probes included on the commercial arrays may not even have any baring on gene transcription, or at best minimal.

Even if you wanted to summarise these to gene level, you don't require any 'tool' to do it. Just use a summarisation function, like min, max, mean, or median. In R, you could just use aggregate(). Be aware of the biological interpretation / meaning of doing this, though.


ADD COMMENTlink written 22 months ago by Kevin Blighe61k

Hi, Kevin,

Thanks for your reply!

I really need this information to do some analysis. Can I use the pipeline described on this web page to do this thing? Weather it is better than those summarisation functions?



ADD REPLYlink modified 22 months ago • written 22 months ago by Wayne Lee10

Hey Wayne. It seems okay, i.e., the Methylation Preprocessor. I mean, it's from the Broad Institute, which is a trusted organisation that has already worked on TCGA data.

ADD REPLYlink written 22 months ago by Kevin Blighe61k

Vary thanks, Kevin! Your answer helped me a lot.

ADD REPLYlink written 22 months ago by Wayne Lee10
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