Centrality Measures in Protein Interaction Networks

Question

[anz]

Hi, I am doing a small study on protein interaction network. Once I prepare the network, and use some Network Visualizer (like Cytoscape), I can get some network features. I wanted to know about the significance of these network values like node degree and centrality measures such as Betweenness Centrality, Closeness Centrality, etc. Also, How to get the load scores of such a network from these data?

I hope my question is not be ambiguous.

Answer 1

[scooter]

Greetings!

There are lots of sources for the understanding the various measures in the literature, but a short version can be found in a tutorial we give: https://cytoscape.org/cytoscape-tutorials/presentations/intro-cytoscape-2022-ucsf.html#/12 that describes the various measures and how to think about them. Briefly: \

• Degree gives you information about how many nodes connect to this node -- nodes with high degree (compared to the rest of the network) are considered hubs. Biologically, this could be a critical protein and perturbation of this protein might be lethal.
• Closeness centrality measures how close, in terms of hops or weighted hops, a node is to all of the other nodes in the network. Perturbations of this node might quickly be felt elsewhere in the cell.
• Betweenness is a measure of the number of paths that pass through this node. Biologically, perturbations of this node might disrupt pathways.

Hope this helps!

-- scooter