creating cytoscape using GO ids

Question

[riyaannmathews]

I'm having a list of GO terms with their semantic relation valuues. I need to do the network analysis using cytoscape for this file.Here one single GO term is associated with many genes. How to create the input file?Is there any direct method or can anyone help me with the creation of the excel file with the corresponding gene symbols.?

[Jean-Karim Heriche]

What you're asking is unclear. What kind of analysis do you want to do ? Do you want to analyze the network of GO terms as implied by your first two sentences ? Or do you want to analyze a GO term to gene bipartite graph as could be implied by your mention of the GOterm gene links ? Using Excel for this is anyway a bad idea.

[LLTommy]

I agree with Jean, but I post a couple of more questions for you to think about. What kind of network analysis do you want to do? Do you 'just' want to display the GO terms and their relationships? Or do you want to analyse them? And if so, how? So also as Jean mentioned, is this about the ontology terms them self or do you have additional data to go with these terms? What is your goal?

[riyaannmathews]

I wanted to do the network analysis of the GO terms using cytoscape

[LLTommy]

Well you have some answers already.so all I might add is: Why cytoscape, is there a reason for your choice? It is one option of course, but if you are familiar with another language but not with javascript you could of course also look for other solutions. So is there a reason why you want to do it with cytoscape or is that just the first thing you stumbled across?

P.S.:Even though I do not suggest it nor tried it, but I just googled for fun 'network analysis Excel' and there actually are hits and poetentially plugins.

[Jean-Karim Heriche]

There's no need to program to use Cytoscape, it has a nice enough GUI. Maybe you're confusing it with cytoscape.js which is written in javascript (Cytoscape is written in Java). Using Excel is a bad idea, see also here.

[LLTommy]

oh yeah, I did confuse it with cytoscape.js! Thanks for that, I have to be more careful.

Anyway, I never said no one should use Excel. I was simply amazed that people actually did plugins for network analysis in Excel - and I wanted to share that with you - I know you love these spread sheets. :D

Answer 1

[Jean-Karim Heriche]

If you want to work on the graph with GO terms as nodes and you already have a matrix of semantic similarity between terms, just convert this matrix into a format that Cytoscape can read e.g. in SIF format: term1 (tab) term2 (tab) similarity value

Answer 2

[Lila M]

If you have the gene ID, you can do the network analysis using ClueGO