A colleague biologist defined a PPI network of several dozen proteins.
He now wants to statistically test if the network is connected more than generally found in the human interactome.
We look for a tool or method that can compare the custom network to other (randomly sampled?) networks (BioGrid? other accessible data?) of the same size and test the connectivity degree and density.
We apparently need tools to subsample the full interactome in a smart way, and compare the obtained 1000+networks to his by looking into network connectivity metrics. Then a statistical test to compare the results and spit out some score of quantile position.
Any ref, hint, link to R-code would be just great.
Thanks in advance for your expert advices
Spectral affinity in protein networks
http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-3-112
Tool Link: http://gaussian.bu.edu/pnns.html
Determining minimum set of driver nodes in protein-protein interaction networks
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0591-3
Tool Link: https://github.com/Zhangxf-ccnu/CC-MDS
Thanks a lot Bipin, the first one is very interesting with the pagerank affinity metric that is worth trying in this case. The second sounds more predictive and we need analytical tools rather than refining predictions (but I will read it all to be sure).
Best
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