Question: network related question
gravatar for ektabundel
3.1 years ago by
ektabundel0 wrote:

hii, i have a list of proteins(125), and protein protein interaction data from string. i want to see my list of protein in protein-protein interaction through cytoscape means i want to see my protein interaction in string dada which i had downloaded. please help me how i can do this in Cytoscape

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ADD COMMENTlink modified 3.1 years ago by Lars Juhl Jensen11k • written 3.1 years ago by ektabundel0

I think I'm right in saying that STRING doesn't just predict protein-protein interactions. It will consider 2 proteins/gene ID's connected if they appear in pubmed journals together for example. Doesn't necessarily mean they're interacting - might be something to be aware of.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Joe16k

Certainly, STRING is not limited to physical interactions. It aims to link proteins together that are likely to function together, which may or may not mean that they physically interact.

ADD REPLYlink written 3.1 years ago by Lars Juhl Jensen11k
gravatar for Lars Juhl Jensen
3.1 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

I am not sure I understand your question.

If what you want to do is to show a STRING network for 125 proteins in Cytoscape, that is easily accomplished with the Cytoscape STRING App. Just install the app, go to File->Import->Network->Public Databases, select "STRING protein query", paste in your 125 proteins, select your desired confidence cutoff, and go through the identifier disambiguation step as you would in the STRING web interface. After that you should see the STRING network in Cytoscape, even looking very much like it does in the web interface.

If what you are trying to do is something more specific to Cytoscape, you will probably have more luck asking the Cytoscape help desk on Google Groups.

ADD COMMENTlink written 3.1 years ago by Lars Juhl Jensen11k
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