Question: project tophits onto a public PPI (protein-protein interaction) dbase to identify neighbours
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gravatar for Abhishek Pratap
3.1 years ago by
United States
Abhishek Pratap170 wrote:

I want to project the identified tophits genes(RNA-Seq) and proteins(proteomics MS/MS) onto a network of protein-protein interaction dbase and zoom into regions that are 1-2 degree away from our search proteins.  I am pretty positive this should be a solved problem in BioC space. Before I spend too much time I thought I will check here.

What have I done so far?

1. got the dbase of PPI from irefindex.org . Is there a better and updated resource for human PPI

2. explored igraph package for doing the analysis. However, I did not find tutorials that showed how to search a giant PPI network for some proteins and zoom into sub-network 1-2 degrees from search proteins.

Appreciate any pointers. 

 

PS: I posted a similar question on biostars

-Abhi

network analysis igraph ppi • 408 views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Abhishek Pratap170
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