node degree in cytoscape to find hub proteins

Question

[rajasekargutha]

Hi, I am working on protein interaction network using cytoscape. 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 decide the hub proteins with these values.

I hope my question is not be ambiguous.

Answer 1

[Diwan]

In cytoscape, you can use "network analyzer" which will be available as default and run "analyze network". It will calculate all properties of network. Hubs are the nodes with higher (more) degree i.e., nodes with more connections. Just sort the output list by degree and you can identify hub nodes. Betweeness centrality (communication hot spots) are nodes that connect distinct parts of the network.

Check this: http://manual.cytoscape.org/en/stable/Network_Analyzer.html

You might find the "PPI network analysis" part of this paper useful: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3143-y

[rajasekargutha]

How to colour only hub protein nodes with different colour

[Diwan]

Just add a new node property and fill it with 1's and 0's, i.e., put hub nodes as 1's. Then in cytoscape, viewer panel, you can color according to this property.

If there are few nodes, just select them manually and override default color for that hub node only. HTH

Another way to highlight a hub is to alter node size and make them bigger than rest of other nodes.

[Kevin Blighe]

Good answer by Diwan. A colleague of mine has recently been using Network Analyzer in order to derive vertex/node degree, BC, and other metrics.