I have two sets of co-expression network, set 1 and 2. Set 1 has been built by combining a number of different microarray datasets corresponding to one developmental process. Similarly, set 2 has been constructed by meta-analysis of a different set of microarray studies corresponding to another developmental process. I want to find the commonalities and differences (which are only due to the developmental processes) in the two network. Any idea/ tool/algorithm or paper reference will be greatly appreciated.