Identifying hub nodes

Question

[NS]

Hi all,

Just to clarify, we can use MCODE or Cytohubba to identify the hub nodes based on different algorithms— correct me if I am wrong. Is there a means to identify Hub nodes on the String app? Also, what are the recommended algorithms on Cytohubba to identify the Hub nodes? I have been using degree and betweenness.

Sincere thanks.

Answer 1

[sangram_keshari]

If String app does mean String database here, Then as per my experience you can't find a hub node there. You need to export it to Cytoscape for using different apps to it.

[NS]

Yes, I was referring to the String data base. So that leaves me with MCODE or Cytohubba. Does Network analyser also help with Hub nodes?

[Kevin Blighe]

I moved Sangram's comment to an answer. Yes, please export your STRING network to Cytoscape and then use NetworkAnalyzer plugin. Also, take a look here: A: node degree in cytoscape to find hub proteins

Kevin