Question: How to create gene-gene/ protein- protein interaction network using Cytoscape?
gravatar for mirza
4.3 years ago by
mirza120 wrote:


I have transcriptome data for a rice-microbe interaction study at different conditions. 1. I want to create interaction networks for few sets of genes using cytoscape.
2. I have the fold change for the genes, do I need to do any other analysis or calculation before starting with cytoscape and if these are possible in cytoscape itself. I will be using cytoscape for the first time, so please help me out.

ADD COMMENTlink written 4.3 years ago by mirza120

I have the same question too.Could you please give me some guidance if you have master the way.Thanks a lot

ADD REPLYlink written 4.2 years ago by 9646128580

sorry, I started working on some other data and haven't found the solution yet! but will let u know, as soon as I get it.

ADD REPLYlink written 4.2 years ago by mirza120

Hi guys, I see the querries are posted in like 4 yrs ago. Now, currently I am starting with these work. I also have a list of genes in one column and fold changes from RNA Seq in another column. I simply want to create an interconnected network based on the fol change values. I studied the cytoscape documentation a lot, nowhere is my problem particularly addressed. Not the major question I talked about, but another problem that is preventing me from staring with cytoscape.So, whenever I import a data table, it fails wit a message "Caught exception in execution of task".
Also, // Can the source and the target nodes be the same in setting the data input (just like it happens in STRING) //

ADD REPLYlink written 20 days ago by mukaniruddha1000
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