Question: creating cytoscape using GO ids
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gravatar for riyaannmathews
2.1 years ago by
riyaannmathews0 wrote:

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.?

genome gene • 727 views
ADD COMMENTlink modified 2.1 years ago by Lila M 470 • written 2.1 years ago by riyaannmathews0
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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.

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche18k

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?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by LLTommy1.2k

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

ADD REPLYlink written 2.1 years ago by riyaannmathews0

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.

ADD REPLYlink written 2.1 years ago by LLTommy1.2k

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.

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche18k

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

ADD REPLYlink written 2.1 years ago by LLTommy1.2k
0
gravatar for Jean-Karim Heriche
2.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

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

ADD COMMENTlink written 2.1 years ago by Jean-Karim Heriche18k
0
gravatar for Lila M
2.1 years ago by
Lila M 470
UK
Lila M 470 wrote:

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

ADD COMMENTlink written 2.1 years ago by Lila M 470
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