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Pie Chart view of Gene Ontology percentages

Sorin Draghici sorin at wayne.edu
Wed May 18 08:07:57 PDT 2005


Nathan,

Onto-Express, one of the Onto-Tools,  will do this and much more. The 
Onto-Tools are available at: http://vortex.cs.wayne.edu

Some of the papers describing Onto-Express (all can be downloaded from 
the same site):

Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa and Sorin Draghici. 
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the 
functional design and interpretation of high-throughput gene expression 
experiments <http://vortex.cs.wayne.edu/papers/Onto_Tools_Ensemble.pdf>. 
Nucleic Acids Research, 32:W449-W456, July 2004.

Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen 
Krawetz and Michael A. Tainsky. Onto-Tools, The toolkit of the modern 
biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate 
<http://vortex.cs.wayne.edu/papers/OntoToolsToolkit.pdf>. Nucleic Acids 
Research, 31(13):3775-81, July 2003.

Sorin Draghici, Purvesh Khatri, Rui P. Martins, G. Charles Ostermeier 
and Stephen A. Krawetz. Global functional profiling of gene expression 
<http://vortex.cs.wayne.edu/papers/Onto-Express_V2_proof.pdf>. Genomics 
81(2):98-104, Feb 2003.

Purvesh Khatri, Sorin Draghici, G. Charles Ostermeier, Stephen A. 
Krawetz - Profiling Gene Expression Utilizing Onto-Express 
<http://vortex.cs.wayne.edu/papers/genomics.pdf>, Genomics, 
79(2):266-270, Feb 2002.

Regards,

Sorin


Nathan Salomonis wrote:

>Greetings,
>
>I was wondering if anyone new of a program that will take an input set of
>genes, for example a whole dataset, that is divided into groups (e.g.
>clusters) and not only identify over-represented GO terms in each cluster
>put generate a graphical pie chart showing the percentages of high level GO
>terms aligning with that cluster? Several genome annotation papers display
>this type of output; however I'm not sure if there is a program that
>generates this type of display.
>
>Thanks,
>Nathan Salomonis
>University of California, San Francisco
>Pharmaceutical Sciences and Pharmacogenomics
>
>GenMAPP (Gene Map Annotator and Pathway Profiler)
>http://www.genmapp.org
>
>
>
>--
>This message is from the GOFriends moderated mailing list.  A list of public
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>Web:          http://www.geneontology.org/
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>  
>

-- 
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=


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