Question

Identifying hub nodes

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5.5 years ago

NS ▴ 10

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.

rna-seq protein protein interaction • 3.3k views

ADD COMMENT • link 5.5 years ago by NS ▴ 10

score 3 · Answer 1 · 2018-10-15

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5.5 years ago

sangram_keshari ▴ 260

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 COMMENT • link 5.5 years ago by sangram_keshari ▴ 260

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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 REPLY • link 5.5 years ago by NS ▴ 10

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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 REPLY • link 5.5 years ago by Kevin Blighe 87k