6.4 years ago by
Although what you observed may seem strange, it is a common misconception than differential methylation (DM) analysis will find only find differences where one group is hypomethylated and the other is hypermethylated. The confusion comes from absolute versus relative comparisons; unless there is a priori data measuring the absolute level of methylation, terms like 'hypo' or 'hyper' are always relative comparisons, so you should ask yourself, "relative to what?".
Here's a concrete example.
||Reads in Cell Type A
||Reads in Cell Type B
Suppose more reads implies more methylation. A is hypermethylated relative to B for gene alpha and delta, but A is hypomethylated relative to B for gene beta and gamma. Note that in each case the difference is 4-fold in one direction or the other. So based on a DM analysis, all of these genes would be DM between the cell types (suppose they had a low q-values so we could call them DM).
Now what if you believed that values greater than 50 implied something was methylated, so that you could make absolute statements like "alpha in cell type A is methylated". Then you might expect MEDIPS to only report alpha and beta as DM. What do you make of delta and gamma then, you ask (at least I think you do because that is how I interpreted your original question)?
Well, delta is NOT methylated in either cell type, but cell type A does have a greater propensity for methylation than cell type B, so much so that MEDIPS would call it DM.
Similarly, gamma is methylated in both cell types, but much more so in cell type B than cell type A.
I hope this helps a little.
modified 6.4 years ago
6.4 years ago by
jwade44 • 10