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

Sorin Draghici sod at cs.wayne.edu
Tue Aug 21 16:15:58 PDT 2007


Dear Dan,

Before you dive into the tens of tools listed on the GO website, you may
want to have a look at this paper:

Purvesh Khatri and Sorin Draghici. Ontological analysis of gene
expression data: current tools, limitations, and open problems.
Bioinformatics, 21(18):3587-95, September 2005.
http://vortex.cs.wayne.edu/papers/Ontological_analysis.pdf

Best regards,


Sorin Draghici, Ph.D.


Director of the Bioinformatics Core, Karmanos Cancer Institute

Associate Professor		Tel: (313) 577-5484
Dept. of Computer Science	Fax: (313) 577-6868
Wayne State University
5143 Cass Ave, Room 431 State Hall,
Detroit, MI, 48202
WWW: http://vortex.cs.wayne.edu/Sorin/ (personal)
WWW: http://vortex.cs.wayne.edu/Projects.html (lab)


Check out my recent book: Data Analysis Tools for Microarrays:
http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc=



Kimberly Van Auken wrote:
> Dear Dr. Villeneuve,
> 
> Thank you for writing to GO.
> There are a number of publicly available tools for displaying and
> visualizing the results of
> your analysis within the context of the GO hierarchy.
> A list of all GO tools, organized according to their use, is maintained
> on the GO's web site:
> 
> http://www.geneontology.org/GO.tools.shtml?all
> 
> Those tools specifically designed for expression/microarray analysis are
> listed here:
> 
> http://www.geneontology.org/GO.tools.shtml?all#micro
> 
> 
> 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.
> 
> If you aren't on the GO Friends mailing list and would like to sign up,
> here is a link to information
> on the consortium's mailing lists:
> 
> http://www.geneontology.org/GO.mailing.lists.shtml?all
> 
> 
> Best,
> Kimberly Van Auken
> Database Curator, WormBase
> 
> http://www.wormbase.org
> http://www.geneontology.org
> 
> 
>> 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.
>>
>> ___________________________________
>> Dan Villeneuve, Ph.D.
>> U.S. EPA  Mid-Continent Ecology Division
>> 6201 Congdon Blvd.
>> Duluth, MN  55804-2595
>> T:  218-529-5217
>> F:  218-529-5003
>> E-mail:  villeneuve.dan at epa.gov <mailto:villeneuve.dan at epa.gov>
>>
> 
> 
> -- 
> This message is from the GOFriends moderated mailing list.  A list of
> public
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> 
> 


--
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