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)?
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.
How about functional networks based on mutual exclusivity?
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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Ok, wasn't sure it if fit your goal. But I did a blog post and tip on GRAIL here too: http://blog.openhelix.eu/?p=3037
Interesting, thanks! For reference, the paper describing the GRAIL method is here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000534, which as Mary mentions is based on literature coexpression (in 250k PubMed abstracts).