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How to create a SIF file to use in Cytoscape?
We have a list of genes symbol considered significant, that I want to visualize in Cytoscape to see their netword and interaction. Though cytoscape needs to be run from a SIF file, I understand perfectly what a SIF file is, we have 500 genes and can't fill out their interaction and target one by one. Is there a program that output a SIF file from a list of genes? Or is there any other program that can output a file compatible with Cytoscape from a list of gene symbols?
cytoscape interaction gene
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by madkitty madkitty

Hello I am using Cytoscape, I have similar question that you asked. Did you solve it? I tried string and save file as xml, but cytoscape does not accept xml. Please if you have update, can you tell me the solution? Best Shaima

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written by saj98 saj98

1 answer

* copy+paste your list in http://string-db.org/ ("multiple names")

* validate

* save -> psi/xml

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you a million!!

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written by madkitty madkitty
I just had a look at the string-db.org link, though our genome isn't in the list. If I select "auto-detect" will it affect the output?
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written by madkitty madkitty

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