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[gofriends] Re: Fwd: Tools to Visualize/Display GO Terms

florian at genomics.princeton.edu florian at genomics.princeton.edu
Tue Aug 21 15:08:55 PDT 2007


Hi everybody,

for visualization you might want to check out
http://function.princeton.edu/GOLEM/

"GOLEM: An interactive, graphical gene-ontology visualization, 
navigation,and analysis tool  on the web. GOLEM is a useful tool which 
allows the viewer to navigate and explore a local portion of the Gene 
Ontology (GO) hierarchy. Users can also load annotations for various 
organisms into the ontology in order to search for particular genes, or 
to limit the display to show only GO terms relevant to a particular 
organism, or to quickly search for GO terms enriched in a set of query 
genes."

Additionally (but maybe not that user-friendly) the R-packages GOstats 
and topGO also display their results on the GO graph.

Hope that helps,
Florian

-- 
Florian Markowetz

Princeton University
Lewis-Sigler-Institute, Carl Icahn Lab
Princeton, NJ, 08544

609-258-8236 (lab phone)
609-258-8004 (fax)
florian at genomics.princeton.edu
http://genomics.princeton.edu/~florian


Quoting Mary Dolan <Mary_Dolan at umit.maine.edu>:

> Kimberly Van Auken <vanauken at caltech.edu> on Tuesday, August 21, 2007 
> at 4:00 PM -0500 wrote:
>> I have also forwarded your email to the GO Friends mailing list, as
>> members of this list may be
>> able to help you evaluate which tool is best suited to your needs.
>>
>>> From: Villeneuve.Dan at epamail.epa.gov
>>> <mailto:Villeneuve.Dan at epamail.epa.gov>
>>> Date: Tue, 21 Aug 2007 13:30:32 -0500
>>>
>>> Hello,
>>>
>>> I have used GeneSpring to analyze a set of zebrafish microarray data.
>>> As part of this analysis, I generated a list of GO categories/terms that
>>> were significantly enriched for my list of differentially expressed
>>> genes.  I am looking for a way to display the list in a tree-like format
>>> that shows the hierarchy of the GO categories on the list.  I tried
>>> submitting the list using the Advanced Search option but this doesn't
>>> show the tree-like structure.  Is there a way to accomplish this using
>>> AmiGO website, or do you know of other publicly available software that
>>> could be used?
>>>
>>> Any assistance you could provide would be appreciated.
>>
>>
> Dear Dr. Villeneuve,
> Here at MGI we have a prototype tool that I think would be of use to you:
> http://proto.informatics.jax.org/prototypes/GOTools/web-docs/GO_showselect_ids.html
> This returns the GO DAG image with your selected nodes indicated in 
> blue in both png and svg format -- you can also download a .dot file 
> that can be used with GraphViz.
>
> I hope this helps.
> Cheers,
> Mary
>
> Mary E. Dolan, Ph.D.
> ************************************
> Mouse Genome Informatics Consortium, The Jackson Laboratory
> mdolan at informatics.jax.org
> (207)288-6439
>
> Research Faculty, NCGIA
> Department of Spatial Information Science and Engineering, University 
> of Maine
> Boardman Hall 329
> University of Maine
> Orono, Maine 04469
> fax: 207.581.2206
> mary_dolan at umit.maine.edu
> ************************************
>
>
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