Cytoscape for co-occurence network analysis
Entering edit mode
6 days ago
Bioinfonext ▴ 330

I am able to import the network into Cytoscape. Now I am trying to find the hub microbes in the network based on Betweenness Centrality and Closeness Centrality.

Just some more queries;
1) How should I import edge attributes (correlation & P-value) as local or shared?
2) How can I do filtering based on cor and p-value (edge attributes) and how to color positive and negative edges?
3) How can I identify the hub microbes in a network (based on network topology calculation)?

Many thanks,

Microbiome 16S analysis Cytoscape Network • 121 views
Entering edit mode
3 days ago
Scooter ▴ 80

Answered on the cytoscape-helpdesk here:

Here is the answer (so those with a similar question don't have to search for it):

Hi Yogesh, Glad you got the network in!

  1. I would always import your edge attributes as shared unless you know that they won't apply if you make sub-networks from your network. In your case, I'm pretty sure they will apply.
  2. As far as filtering, go to the filters tab in the control (left) panel, add a Column Filter and choose the correlation and/or p-value columns. You can add multiple filters and create boolean expressions -- for example, you could look for only edges that have p-value < 0.05 AND correlations > 0.6, or whatever makes sense for your data.
  3. You can calculate the topology by going to "Tools->Analyze Network".

-- scooter

Entering edit mode

Thank you so much Scooter. sorry for the cross-post.


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