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Applications Of Gene/Protein Networks

I'm interested in seeing papers that describe useful applications of gene/protein networks (for example, in the analysis of transcriptomics studies). The catch is that I'm only interested in networks other than those based on physical protein interactions and gene co-expression. What other kinds of networks are available (and useful)?

network reference
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updated by David Quigley David Quigley • written by Andrew Su Andrew Su

3 answers

What about literature-based functional connectivity like this paper shows?

http://www.nature.com/ng/journal/v41/n12/fig_tab/ng.479_F2.html#figure-title

That may be based in the underlying papers on co-expression or ppi, but for the purposes of the GRAIL tool it's literature that forms this.

Have to get into a meeting, will look back later.

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updated by Ram Ram • written by Mary Mary

How about functional networks based on mutual exclusivity?

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written by Chris Miller Chris Miller

There is a large literature on genetic interaction networks. One way to generate these networks is to generate a library of two-way gene knockouts and look for effects on a phenotype (e.g. viability or growth in yeast). Look at the work from Trey Ideker's, Nevin Krogan's, and Charlie Boone labs for a start. The Ideker lab's web site is helpful as a systems biology overview.

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written by David Quigley David Quigley

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