I am working on a Boolean network (GRN) I built from genes that are differentially expressed. Now I have to identify the key genes for the process I am studying. How do you go about that? Is there some "standard" pipeline for doing this?
- I know I can analyse the topology of the network, and rank the genes based on their metrics (centrality, degree etc). I can also find strongly connected components, modules etc. For this I know Cytoscape and its plug-ins/apps will do.
- Another approach would be to simulate the dynamics on the network, but I don't know what people usually do in this case. What is your preferred tool? And what information could I get from this simulation?
I have the feeling that people are mainly playing around with metrics and filters and keep the ones which give the results they want or something that is already known, instead of following a rigorous approach.