Question: How to visualize Proteome Networks
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gravatar for Pranavathiyani G
2.5 years ago by
Pondicherry, India
Pranavathiyani G300 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 2.5 years ago by arta580 • written 2.5 years ago by Pranavathiyani G300
1

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

ADD REPLYlink written 2.5 years ago by TriS4.2k
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 2.5 years ago by Jean-Karim Heriche22k

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

ADD REPLYlink written 2.5 years ago by Pranavathiyani G300

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

ADD REPLYlink written 2.5 years ago by Jean-Karim Heriche22k

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

ADD REPLYlink written 2.5 years ago by Pranavathiyani G300
0
gravatar for arta
2.5 years ago by
arta580
Sweden
arta580 wrote:

Did you try gephi ?

ADD COMMENTlink written 2.5 years ago by arta580

Visualization of large scale networks depends on hardware components also?

ADD REPLYlink written 2.5 years ago by Pranavathiyani G300

Of course, but i am not expert about it.

ADD REPLYlink written 2.5 years ago by arta580
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