project top genes/proteins on a Protein-Protein Interaction (PPI) network map

Question

[Abhi]

Hi Folks

Posting here after a long hiatus. We have identified diffExp genes (RNA-Seq) and proteins (MS/MS proteomics exp) for various drug treatments on cell lines.

Just wondering whats tools are available for quickly building (more so using) an available Protein-Protein Interaction dbase for projecting top genes/proteins from our analysis to understand the network characteristics such as hubs, how close/far are hits from our genomics and proteomics derived top hits.

Thanks! -Abhi

Answer 1

[Jean-Karim Heriche]

I would use the iRefIndex protein interaction data. It integrates protein interactions from many different databases. You can download the graph directly from within Cytoscape 3.x but for the type of querying you want to do, I would use the igraph R package.