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