Background in Enrichment of DMRs

[Tommaso Andreani]

Hello,

I have my set of Hyper and Hypo DMRs from my experiment.  I would like to enrich with great tool (http://bejerano.stanford.edu/great/public/html/) the DMRs of each category (Hyper or Hypo). Since I have to select a back ground I wounder which one I have to use.

For example I decided to take DMRs with a minimum of 3 CpG as it make sense that for a region to be differentially methylated it requires at least a minimum nunber of CpG. Is it possible to take as background all the regions output of the dmr command and as a universe the DMRs I select with a minimum number of CpG?

Thanks in advance for clarification

Tommaso