What are the possible ways that I could compare two Gene interaction Networks?
WT upregulated genes interaction network vs Mutants upregulated genes interaction network
Mutants upregulated genes interaction network
To some extent, it depends on what you're interested in. What biological question(s) are you trying to address?
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.
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