find interactions among genes

Question

[??]

Hi,

I wonder are there some software or web tools available to check or visualize the interactions between a list of genes(about a thousand)?

Answer 1

[komal.rathi]

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

[komal.rathi]

Are you talking about the stand-alone version or the cytoscape plug-in?

[??]

I was referring to that of plug in

[komal.rathi]

You can read this and this. Also, this is a good step-by-step tutorial.