Question: Identifying hub nodes
1
gravatar for NS
6 months ago by
NS10
NS10 wrote:

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.

ADD COMMENTlink written 6 months ago by NS10
2
gravatar for sangram_keshari
6 months ago by
sangram_keshari130 wrote:

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.

ADD COMMENTlink written 6 months ago by sangram_keshari130

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?

ADD REPLYlink written 6 months ago by NS10

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

ADD REPLYlink written 6 months ago by Kevin Blighe41k
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