Pathway analysis - (Dec/22/2016 )

Hi,

I need some advise on what I should do. I've got some microarray data and I've compared my different control and treatment groups and pulled up a big list of genes that we might be interested in that are differentially expressed. My supervisor suggested getting pathway analysis done on these genes to see what we should concentrate our efforts on. We gave the gene list over to someone to run it through IPA and now I've got 5 possible interesting networks to look at...

This might sound stupid, but I'm at a loss as to what to do with this network list. There's still heaps of genes there. I am out of my depth here.

I would start by looking at the networks and seeing where your target might interact - STRING (string-db.org) might be some help here, and how significant this interaction is. You will need to work out where your target interacts (upstream? downstream?) and the potential outcomes of this interaction.

You can then prioritize targets based on available readouts - protein expression, RNA levels, and that sort of thing.