I wonder are there some softwares or webs available to check or visualize the interactions between a list of genes(about a thousand )?
You can use GeneMANIA. Though I'd recommend Cytoscape (and it has a GeneMANIA plugin as well).
thanks. I actually am using cytoscape. I used clueGO+cluePedia. (the network resulted from this app gave me the relationship between functional groups , but i did not think the interaction was indicated by node connections)
i am just going to try out Mania. Are you familiar with this app. is the network presented based on the interactions?
further what file does MANIA recognize? i cannot load my excel or test files
Are you talking about the stand-alone version or the cytoscape plug-in?
I was referring to that of plug in
You can read this and this. Also, this is a good step-by-step tutorial.
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