MCODE cytoscape analysis
Hello all, I hope you all are doing good. I have made clusters of a string PPI network using MCODE from cytoscape but I am not sure how to do the analysis? How do I evaluate the significance of the clusters obtained? Is the highest scoring network considered the best? This is the first time I am doing clustering. Would really appreciate it if someone could take out their valuable time to help me. Thank you.
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Bioinformatician_in_trouble •
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You may have seen these already, but there are tutorial and documentation links from both the MCODE app and clusterMaker2 apps, which can each perform MCODE clustering:
If you are asking about MCODE clustering in general, perhaps this paper is a good place to start: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-2