How to visualize Proteome Networks

Question

[Pranavathiyani G]

How can I visualize whole proteome network for any particular organism? Is there any tool or software for this. Cytoscape is one of the tool for visualization of networks, but is there any tool for large scale network visualization?

[TriS]

this might help: https://www.hindawi.com/journals/abi/2017/1278932/

[Jean-Karim Heriche]

What are you trying to achieve ? A whole proteome network visualized as a graph is just a gigantic, useless hairball. One is rarely interested in this but usually on specific aspects of the network. For example, you might be interested in how different cellular processes are connected, in which case, you could cluster/collapse proteins into nodes representing the processes they are involved in and link processes that share members.

[Pranavathiyani G]

So, I can cluster nodes based on GO? Will that make sense?

[Jean-Karim Heriche]

Yes but this only makes sense if this is relevant to the context or biological question you're asking.

[Pranavathiyani G]

I wish to analyze in context to disease & gene expression.

Answer 1

[arta]

Did you try gephi ?

[Pranavathiyani G]

Visualization of large scale networks depends on hardware components also?

[arta]

Of course, but i am not expert about it.