How could I compare two Gene interaction Networks?

Question

[WUSCHEL]

What are the possible ways that I could compare two Gene interaction Networks?

WT upregulated genes interaction network vs Mutants upregulated genes interaction network

[Jean-Karim Heriche]

To some extent, it depends on what you're interested in. What biological question(s) are you trying to address?

[lessismore]

Few things you can compare:
- genes with top degrees across the two networks (+ other network metrics)
- the functional enrichment of the gene modules that you believe can be interesting
- functional enrichment of the interactors of the DE genes
As a general rule, focus on genes in the pathways you're interested in.