Building and analysing PPINs
Now that we know a bit about graph theory and protein-protein interaction networks, we can look at the steps, strategies and tools used to build and analyse these networks (Figure 20).
Figure 20 A potential workflow for building and analysing protein-protein interaction networks.
First, we will briefly introduce various software packages or programmatic methods used to build and analyse networks. Next we talk about sources from which you can obtain PPI data and discuss several ways of analysing the data of which topological analysis of centralities and community-finding approaches are common strategies. Finally, we look at ways in which additional data can be added to understand the biological context of the network.