ClueGO basics

[Pankaj Chopra]

Hi,

I am trying to use ClueGO (in cytoscape) to visualize results obtained from the GO website.

With my data (GOID.input.png & GOID.genes.png attached), I would like to:

1. View the significant GO terms as a node and edge graph. I believe the ClueGO documentation section "ClueGO visualization of preselected GO terms and pathways" is what I require. I copy and paste my GOID and pvalue data (input 'GOID.input.png' in attached xls) into ClueGO. I use all default settings except:

Analysis Mode: Preselected Functions
ClueGO Settings > Ontologies/Pathways: GO Biological Process

and then I click on start. However, I just get the nodes without any edges (see attached screenshot 'ClueGO.terms.png'). What do I need to do to get the interconnections between these GO terms and to get the size proportional to the pvalue?

2. For each significant GO term, I have a set of genes that I wish to visualize (input format 'GO.genes.png' attached). I wish to visualize these such that the GO terms are the nodes, and the edges are the GOterm-gene associations. How should I go about doing this? Any pointers/tutorials/website would be highly appreciated.

Thanks!

Pankaj

[Scooter Morris]

Hi Pankaj,

    Unfortunately, your attachments didn't come through for some reason.  Perhaps you could try and post them again, or better yet, I would send mail to the ClueGO authors -- they are usually very responsive.

-- scooter