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Are these epigenetic signatures?

Posted by gui11aume on 01 Dec 2013 at 13:46 GMT

The Results section mentions "Interestingly, the majority of each DMR set was specific to an exposure group and not common with the other exposure DMRs", leading to the conclusion that "each exposure had a unique signature of epigenetic alterations in the F3 generation sperm."

However, I don't see in the text any measure of the statistical significance of this specificity. Here the total number of DMRs is small compared to the number of regions on the array. So if the perturbations of the methylation patterns are random (uniform), very little overlap is expected in the first place. In this respect, the most surprising result is the overlap between the DMRs induced by pesticide and plastics. The significance of the overlap between two sets (or lack thereof) is usually quantified by the Fisher's exact test, or by the hypergeometric distribution.

Another way to support the claim that different exposures induce different epigenetic signatures would be to show that identical exposures induce identical DMRs. However, the 3 replicates were pooled before they were compared to each other. The same kind of diagram and analysis could be carried for individual replicates.

No competing interests declared.