Methylation and Expression correlation

[balaji]

I have 3 samples and I am doing a analysis on 2 samples to identify correlated/anticorrelated genes.
I have identified some differentially methylated genes while comparing sample1 and sample2, i want to correlate the methylation values against expression values in sample1 and sample2. And then describe if the gene is correlated or anti-correlated. I would like to have some r (correlation value)and p-values from these comparisons. Is it possible to get some other statistics measure to identify significant genes.
I hope I explained it clearly. Thank you for your help.
Updated: I am working with mouse species

[simonandrews]

You need to be careful with this type of analysis as it's really easy to get false correlations. The big problem is CpG islands. These are generally unmethylated and genes with CpG islands are generally higher expressed than those without so across all genes you get a negative correlation between promoter methylation and expression, but it's far from clear that there is any causal link between the two.

If you're going to do this kind of analysis I'd recommend either doing the analysis separately in CpG island containing genes, or finding some way to account for this potential bias in your stats. Frankly, our experience has been that outside some specific examples (oocytes are the best one, where there is a positive correlation between expression and methylation in both gene bodies and promoters), that the linkage between methylation and expression is greatly exaggerated.

[chadn737]

What species are you working in? Methylation is very context specific.