Question

How to create a SIF file to use in Cytoscape?

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11.2 years ago

madkitty ▴ 690

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 • 8.0k views

ADD COMMENT • link updated 11.2 years ago by Pierre Lindenbaum 166k • written 11.2 years ago by madkitty ▴ 690

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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

ADD REPLY • link 9.7 years ago by saj98 ▴ 140

score 2 · Answer 1 · 2014-09-04

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11.2 years ago

Pierre Lindenbaum 166k

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

* validate

* save -> psi/xml

ADD COMMENT • link 11.2 years ago by Pierre Lindenbaum 166k

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Thank you a million!!

ADD REPLY • link 11.2 years ago by madkitty ▴ 690

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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?

ADD REPLY • link 11.2 years ago by madkitty ▴ 690