Top 3 gene clusters using MCODE in Cytoscape - Protein-protein interaction analysis

Question

[bioinformatics]

Hi everyone,

I am trying to find the top 3 gene clusters using MCODE in Cytoscape by performing cluster analysis. I have imported STRING data on a differentially expressed gene from this link.

https://string-db.org/cgi/network?taskId=bbmcnhrpg5t6&sessionId=bRcZqRm8SEiC

I've used the parameters, node score cut-off =0.2, degree cut-off =2, k-score = 2, and max depth = 100.

My screen ended up with this result. Does anyone know what the next steps are and how I export the results?

Also what do the results mean?

Thanks in advance.

Answer 1

[xanderpico]

Hi. I have a couple tips and answers for you...

• Instead of going to the STRING website, performing a query, exporting and importing into Cytoscape, you can simply use the stringApp in Cytoscape to perform queries and construct networks with a ton more information and detail: https://apps.cytoscape.org/apps/stringapp (see tutorials if not clear)
• MCODE and other topology based clustering (like MCL) is really only useful when you have a massive network with complex, varied connectivity. These algos will identify highly intra-connected subnetworks within your network and list them from largest to smallest for you to continue working with (e.g., data overlays).
• In your example, you started with simple network of 11 nodes, evenly connected. So, MCODE returned the entire network as the only "subnetwork" it could find. There are no subnetworks in this tiny network :)