How to simulate knock-downs?

[fkgruber]

Hi
How can we simulate knockdown experiments in SERGIO? I would like to be able to knockdown specific genes and see the effect on the rest of the network.
thanks
FKG

[fkgruber]

I think the ability to simulate knockdown of 1 or more genes is critical to be able to verify things like interactions between genes. FOr example the effect of G1 on G2 may be a function of G3. Our infer network may be predict this sort of interactions but how do we verify this on the ground truth? Since the way the data is so complicated the best would be to simulate knockdowns and verify this sort of interacting effects.

[PlusoneD]

I also think it's important to simulate knockout or knockdown of expression data, and I 'm trying to first change my network and then generate data through SERGIO, which is simplest. I'm also trying for better ideas, which is hard but meaningful. ^v^