On Mon, Dec 26, 2011 at 7:30 AM, judy <happy.p...@163.com> wrote: > how to import the data from “string” to cytoscape？
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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!
On Thu, Dec 29, 2011 at 6:42 PM, judy <happy.p...@163.com> wrote: > 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
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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.
> On Thu, Dec 29, 2011 at 6:42 PM, judy <happy.p...@163.com> wrote: > 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
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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
On Thu, Dec 29, 2011 at 6:42 PM, judy <happy.p...@163.com> wrote:
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
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>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
>On 2012-01-03, at 8:10 PM, Peng-Liang Wang wrote:
>> On Thu, Dec 29, 2011 at 6:42 PM, judy <happy.p...@163.com> wrote: >> 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
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Hi, you could use ClueGO+CluePedia to visualize fast STRING interaction data on the network (http://www.ici.upmc.fr/cluepedia/CluePedia_Fig1_Example.pdf). You can integrate those known interactions with interrelations extracted from your data (CluePedia provides built-in stats for that). Beside this, you can visualize miRNA target predictions and functional annotations on the network using together, CluePedia and ClueGO.
