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I had a set of genes for honey bees. I found the homologues of those genes in the house fly and created a network of the honey bee genes and a network of the homologous fly genes using STRING.

I know that I could do a topological comparison between the networks and check if the same set of genes give the same hubs when in two different species. However, I can't find a single study where something similar has been done.

What biological inference can I draw from the topological parameters? For example, if the diameter of the fly network is smaller than the honey bee network, what inference could I draw?

UPDATE: It would be great if atleast some publications could be given where network comparisons have been done between different species.

The Last Word
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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:

llrs
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gabt
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