Re: [cytoscape-helpdesk] Making networks with my own list of proteins

[Alexander Pico]

I forwarded your question to the PSICQUIC google group listed on their website, which I found on this page:
http://apps.cytoscape.org/apps/psicquicuniversalclient

Someone on this Cytoscape list might know the answer as well, but the PSICQUIC list is more direct.

Cheers,
 - Alex



On 6/13/12 1:34 PM, "Gun" <gun...@gmail.com> wrote:

Hello,
I'm a new user of Cytoscape.
I'm trying to make a network with my proteins (about 350 different proteins from my experiment). Using PSICQUICUniversalClient, I wanted to make the networks. After putting all my proteins and starting  the process, I got a results with more than 2000 nodes and 8000 edges from STRING with PSICQUICUniversalClient plugin. Actually, I wanted to make a network only with my proteins, so I expected less than 350 of nodes. (I tried STRING webserver and it made correctly.)
I wonder what is wrong with my process? (I tried both query modes. Both showed the same results.)
Please let me know if anyone has the solution.
Thanks,
Gun

[giovanni scardoni]

Dear Gun,

here, at the Center for BioMedical Computing, we collected a ppi network of more than 12.000 human proteins and 180.000 interactions. 

With the beta-version of our Pesca plug-in we can extract the subnetwork from your list of proteins. 

If it can help, let me know and we will produce your network!

Giovanni 

2012/6/13 Gun <gun...@gmail.com>

Hello,

I'm a new user of Cytoscape.

I'm trying to make a network with my proteins (about 350 different proteins from my experiment). Using PSICQUICUniversalClient, I wanted to make the networks. After putting all my proteins and starting  the process, I got a results with more than 2000 nodes and 8000 edges from STRING with PSICQUICUniversalClient plugin. Actually, I wanted to make a network only with my proteins, so I expected less than 350 of nodes. (I tried STRING webserver and it made correctly.)

I wonder what is wrong with my process? (I tried both query modes. Both showed the same results.)

Please let me know if anyone has the solution.

Thanks,

Gun 

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)

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