Applications Of Gene/Protein Networks
3
2
Entering edit mode
12.9 years ago
Andrew Su 4.9k

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 • 2.7k views
ADD COMMENT
1
Entering edit mode
12.9 years ago
Mary 11k

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.

ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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).

ADD REPLY
1
Entering edit mode
12.9 years ago

How about functional networks based on mutual exclusivity?

ADD COMMENT
1
Entering edit mode
12.9 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1423 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6