Question

find interactions among genes

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9.5 years ago

?? • 0

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)?

gene • 2.1k views

ADD COMMENT • link updated 24 months ago by Ram 44k • written 9.5 years ago by ?? • 0

Ram · Answer 1 · 2015-06-16

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9.5 years ago

komal.rathi ★ 4.1k

You can use GeneMANIA. Though I'd recommend Cytoscape (and it has a GeneMANIA plugin as well).

ADD COMMENT • link updated 24 months ago by Ram 44k • written 9.5 years ago by komal.rathi ★ 4.1k

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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?

ADD REPLY • link updated 24 months ago by Ram 44k • written 9.5 years ago by ?? • 0

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further what file does MANIA recognize? i cannot load my excel or test files

ADD REPLY • link 9.5 years ago by ?? • 0

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

ADD REPLY • link 9.5 years ago by komal.rathi ★ 4.1k

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I was referring to that of plug in

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 9.5 years ago by ?? • 0

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

ADD REPLY • link updated 24 months ago by Ram 44k • written 9.5 years ago by komal.rathi ★ 4.1k