Question: A Tree Viewer Software For The Gene Ontology Terms?
9
gravatar for davidechicco
5.1 years ago by
davidechicco130
davidechicco130 wrote:

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:

enter image description here

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

Thanks a lot!

ADD COMMENTlink modified 3.8 years ago by hfang.shanghai140 • written 5.1 years ago by davidechicco130
10
gravatar for sarahhunter
5.1 years ago by
sarahhunter590
Cambridge, UK
sarahhunter590 wrote:

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

ADD COMMENTlink written 5.1 years ago by sarahhunter590

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

ADD REPLYlink written 12 months ago by inepomuceno0
1
gravatar for akshayb04
4.8 years ago by
akshayb0420
Hannover, Germany
akshayb0420 wrote:

There are cytoscape plugins, one such is ClueGO.

ADD COMMENTlink written 4.8 years ago by akshayb0420
1
gravatar for hfang.shanghai
3.8 years ago by
United Kingdom
hfang.shanghai140 wrote:

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

ADD COMMENTlink written 3.8 years ago by hfang.shanghai140
0
gravatar for Diwan
5.0 years ago by
Diwan510
United States
Diwan510 wrote:

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

ADD COMMENTlink written 5.0 years ago by Diwan510
0
gravatar for quentin.delettre
5.0 years ago by
France
quentin.delettre420 wrote:

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.

ADD COMMENTlink written 5.0 years ago by quentin.delettre420
0
gravatar for yang.robert
5.0 years ago by
yang.robert0 wrote:

cytoscape

ADD COMMENTlink written 5.0 years ago by yang.robert0
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