Clustering App in Cytoscape

[nus]

Hi, I'm trying to create an association between two groups, a candidate gene (group 1 has one gene) with a list of nearly 40 genes (group 2 has 40 genes) that were shown to have associations with the candidate gene through literature search. I would like to have the candidate gene in the centre of the network. Can anyone please suggest how I can create these links with the candidate gene and later use this network for downstream functional analysis. 

Thanks in advance

Nara

[Scooter Morris]

Hi Nara,
    You just want to create a file of the following form:

Candidate\tTarget
gene1\tgene2
gene1\tgene3
....

You'll have 41 lines -- a header line and a line for each of your associated genes.  Then read that in, and you'll be ready to do your analyses and visualizations.

-- scooter

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[Narasimhan Kothandaraman]

Hi Scooter, Thanks. I believe you have to run this in some sort of program or has it to be run using any apps in Cytoscape. I'm not sure how to do it. If you can give me some directions on how to create the file in which interface and to run it, it would be really helpful for me. Or if there is a manual I can go through on how to create the file and run it will help me. Regards, Nara

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[Scooter Morris]

Hi Nara,
    You can just use Excel or any text editor to create the file.  To read it in in Cytoscape use File->Import->Network->File.

-- scooter

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