Compare two networks of the same genes between two species
So, you can give a try to this Cytoscape app that will allow to perform comparison between networks.

This app is not specifically designed for comparing networks across different species but it will enable you comparing any kind of networks.

These are the papers they published, which can give you some hints.

About your specific problem...I can't help you about what to look for when you're comparing networks from different species (not an expert in this specific topic) but as far I know you should look for something related to patterns occurring across different networks (i.e. species), network motifs, distribution of network centralities, conserved structures. In general, to compare networks, I would look for global properties (e.g. diameter, clustering coefficient...) while I would use local properties (e.g. degree, closeness, and network centralities in general) to compare the role of a node that you retrieved in all your networks.

Also, since you're looking for some literature, these links may help:  


About conserved patterns of protein interaction in multiple species
About comparing genomic expression patterns across species
This one is slightly out of topic but can give you
some other ideas about comparing networks.