String network analysis
I have a protein list extracted from microarray data and I am trying to find their interaction together. I got a network from STRING. my question is what should I do after extracting this network, what is the statistical test to be done on this network to show its biological significance.
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mayada_mazher1991 •
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You can try analyzing your protein list with NetworkAnalyst. It allows you to perform ORA enrichment analysis, module detection and several other features on your STRING network. Disclaimer: I am involved with the project.
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Welcome to biostars. There is no need to SHOUT. I have adapted your title to remove the uppercase characters. In addition, note that should have been a "question" rather than a "tool", which is only used for announcing new tools. Please select meaningful tags, as such experts can easily find your question. Logical tags would have been "string" and "network", for example. I have added these to your post.
I’m not sure there really is much to be done with STRING networks. They kind of already are the result. It’s biological significance will largely be down to whether you thing the patterns you’re seeing make sense/tell a cohesive story etc.
Bear in mind that a STRING network isn’t like a pathway analysis etc. It includes things like how often 2 genes have been mentioned together in papers, which is not something you could exactly ‘statistically test’.
You may take some ideas from the work by my colleague, which started as a STRING network that was exported to Cytoscape where further analysis was performed: New insights in Tibial muscular dystrophy revealed by protein-protein interaction networks.
I do generally agree with jrj.healey's sentiment, though.