Identifying interactors of hub genes using Cytoscape Network Analyzer plugin

Question

[ishengomae]

I have used Network-Analyzer Cytoscape plugin to identify hub proteins - nodes with the highest node degree distribution - in my protein-protein interaction networks.

Now I would like to identify nodes interacting with my hub proteins. I want to perform an enrichment analysis (with cytoscape plugin BiNGO) to identify biological processes enriched in relation with my hub proteins.

How can I extract subnetwork cluster consisting of proteins interacting with my hub proteins? I can't seem to work around that task with the NetworkAnalyzer plugin. I would also appreciate if someone could suggest to me other or better alternatives.

Thanks.

Edson

[Diwan]

Networkanalyzer is just to calculate the properties of network. If your goal is getting clusters of subnetwork you can explore other clustering plugins such as clusterviz etc. As Jean has pointed out, if you just want to focus on hub, use the option "select first neighbours of a node" in cytoscape window. Then you can extract all the selected nodes as a separate subnetwork.

Answer 1

[Jean-Karim Heriche]

The cytoHubba plugin for cytoscape 2.x seems to do what you want (I haven't tried it though). With NetworkAnalyzer, you'll have to do it manually, i.e. select one hub then its interactors and export them as a separate graph. Otherwise, once you've identified the nodes of interests, you can extract their interactors with a script.