Question: How to visualize Proteome Networks
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gravatar for Pranavathiyani G
5 months ago by
Pondicherry, India
Pranavathiyani G180 wrote:

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?

ADD COMMENTlink modified 5 months ago by arta450 • written 5 months ago by Pranavathiyani G180
1

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

ADD REPLYlink written 5 months ago by TriS3.3k
1

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.

ADD REPLYlink written 5 months ago by Jean-Karim Heriche15k

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

ADD REPLYlink written 5 months ago by Pranavathiyani G180

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

ADD REPLYlink written 5 months ago by Jean-Karim Heriche15k

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

ADD REPLYlink written 5 months ago by Pranavathiyani G180
0
gravatar for arta
5 months ago by
arta450
Sweden
arta450 wrote:

Did you try gephi ?

ADD COMMENTlink written 5 months ago by arta450

Visualization of large scale networks depends on hardware components also?

ADD REPLYlink written 5 months ago by Pranavathiyani G180

Of course, but i am not expert about it.

ADD REPLYlink written 5 months ago by arta450
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