how to import the data from “string” to cytoscape？

[judy]

how to import the data from “string” to cytoscape？

[Peng-Liang Wang]

Can you give some details?

Peng

On Mon, Dec 26, 2011 at 7:30 AM, judy <happy...@163.com> wrote:

how to import the data from “string” to cytoscape？

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[judy]

Dear Wang：
Hi,thanks for your reply!
First I imported some genes into a web software "String".I had
got the protein interaction networks according the gene
products.now,I'm wanna visualize the networks by Cytoscape and select
the hub genes from the mass of genes. So my question is that weather
I can import the data from "string" into cytoscape? how can I do that?
In fact I had tried to download the file
“network_medusa_HDYkAfh7S__A_dat”from string,but I failed to import it
into my cytoscape.
Look forward to your sincere help......Thanks again!


Judy

[Peng-Liang Wang]

I am not sure if the web software "string" has any connection to this one, http://www.string-db.org/. If this is the case, there is a plugin StringWSClient for Cytoscape, http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=StringWSClient. You can install it through Cytoscape plugin manager.

Peng

[Gary Bader]

Hi Judy,
If you download the "Text Summary" .txt file from STRING (instead of trying the "Graph Layout" .dat file), you can import it into Cytoscape using the table import function (File->Import->Network from Table (Test/MS Excel)...). The first two columns contain the interactions and the rest contain the weights of different interaction types from STRING. Unfortunately, the specific layout of the string network is not easy to import into Cytoscape right now, but the interactions are.

Best,
Gary

http://baderlab.org
The Donnelly Centre - http://www.thedonnellycentre.utoronto.ca/
University of Toronto

[黄东兰]

Thanks for your patience ！I had download the plugin StringWSClient and used it 。I found it just canbe use single gene，eccept multiple genes。But I needs multiple gene's network.Thank you all the same！
Judy

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[黄东兰]

Gary,thanks for your patience!I had successfullly imported the data into cytoscape with your help.

Judy

[wuqi...@gmail.com]

Hi,Peng

I used the cytoscape Clue Go and Clue Pedia for the first time. I have some problem to use it. Can I have a contact with you? Now I am as a visiting scholar in JHU. I can call you if you will give me your phone number.

Best wishes!

Qian Wu

在 2011年12月29日星期四UTC+8上午2时55分44秒，Peng-Liang Wang写道：