What’s the Answer? (in silico knockouts)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is something I’d like to see, and I feel like I have heard examples, but I can’t quite place the possible tools.

A model for in-silico knock-out experiments ?

I want to assess impact of a knock-out experiment using a simiplified in-silico approach. At the moment, I trying to solve the problem by creating a tissue specific network and see various network properties with and without the gene (that knocked out) and its vertices. Is there any better way to do it using a more robust network/systems based method or something similar to synthetic lethality for non-cancerous phenotype ?

Khader Shameer

There’s only one suggestion over there right now. It’s bugging me because I feel like there’s something I can vaguely remember having read or seen and can’t seem to pull it out of my memory banks. Anyone got any leads on this? I can really see the utility of this idea. If you know, go add your thoughts to the answers.