A Tree Viewer Software For The Gene Ontology Terms?

Question

[davidechicco]

I have some lists of gene annotation come from the Gene Ontology. Every annotation is a coupling <gene, feature> where the feature is a Gene Ontology term. Every term is a node in the Gene Ontology tree.

I need a tree visualization tool to depict the Gene Ontology tree of that term, and so understand in which tree level is the analyzed term.

Something like this picture:

Can you suggest a tree viewer software that could be useful to me to solve this issue?

Thanks a lot!

Answer 1

[sarahhunter]

Hi,

You're not looking for a tree viewer, you're looking for a DAG viewer ;-) In your example, if it were a true GO graph, E would, for example, be a child of D and I.

The EBI's QuickGO tools allows you to do what you want.

For example, I selected a few terms that were related to Apoptosis and generated the following ancestor chart for comparison: http://www.ebi.ac.uk/QuickGO/GMultiTerm#a=64%240AaC0E%5Bq0Nkg&tab=chart&c=

Instructions:

1. Go to the QuickGo website home page Near the top of the page, there is a search box with the "QuickGO" logo next to it. There are also the links "Web services", "Dataset" and "Term Basket".
2. Click on Term Basket and it will open a popup.
3. In the textarea, enter the list of GO terms you would like to visualise (new-line delimited works OK) and click on the "add to basket" button - these terms will appear as a list at the top of the popup
4. At the bottom of the popup there are a number of other buttons - "Use terms", "Display terms in ancestor chart", "find annotations", etc. If you click on "Display terms in ancestor chart", it will load a visualisation of how these terms relate to one another. Note that if the terms are from the the 3 different ontologies (MF, BP, CC) they will be displayed in different charts and you may need to scroll to see them all.

Hope this helps!

Sarah

[inepomuceno]

Hi Sarah,

can I do this graph viewer automatically using R? I need to do this picture for several groups of GO term and I would like to do it using an script automatically.

Thanks in advance

Isabel

Answer 2

[akshayb04]

There are cytoscape plugins, one such is ClueGO.

Answer 3

[hfang.shanghai]

http://supfam.org/dnet/visDAG.html

Answer 4

[Diwan]

You may want to check FDA's GOFFA tool.

website: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm233315.htm

Paper: http://www.biomedcentral.com/content/pdf/1471-2105-7-S2-S23.pdf

Answer 5

[quentin.delettre]

I built a graph viewer for gene ontologies with D3.js and some python scripts, following this blog post. You can do it too.

I also built a graph viewer with the vivagraph javascript library, it is much more efficient (thanks webgl) but less flexible.

I think there is also some GEPHI tools to do that.

If you are really interested, i can give you some advices.

Answer 6

[yang.robert]

cytoscape