GO Network and Node highlighting in Cytoscape or other tool?

Question

[Alexandros]

Hello everyone,

I am super new here and also new in these kind of analysis. Please bear with me!

I am studying a new organism so I have only predicted genes. I have derived GO terms and other annotations from Blast2GO/eggNOG/blastx homology etc. So I don't have gene names but only GO terms.

I would like to have the full network of my GO terms visualised and then highlight a query GO term(s) in that network.

I was told to do that in Cytoscape (which I dont know yet how to use). However any advise would be super welcome.

Thank you so much.

A

Answer 1

[scooter]

Cytoscape will read in pretty much any text file that defines a network. Essentially, you want to construct a file such that each row represents an edge:

Term1 Term2
Term1 Term3
Term2 Term3
...

What's not clear to me from your description is how you want those terms connected. Typically, a gene will have multiple GO terms associated with it, so you are more likely to do something like:

Gene1 Term1
Gene1 Term2
Gene1 Term3
...

and then you would get a bipartite network between genes and terms. Another way to do the visualization is to construct a network of the GO hierarchy and for each term show how many genes have that annotation.

So, the question becomes -- what are you hoping to see with your network?

-- scooter