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Pie Chart view of Gene Ontology percentages

Jane Lomax jane at ebi.ac.uk
Wed May 18 03:13:34 PDT 2005


Hi Nathan,

At present, there isn't a single program that performs this sort of 
analysis, but it is possible to do. The figures that you've seen in genome 
papers are made using GO slims, which are basically cut-down versions of 
the GO, containing usually just a small number of high-level GO terms. We 
provide a generic GO slim and some species-specific slims here:

http://www.geneontology.org/GO.slims.shtml

Or you could create your own using the ontology editor DAG-Edit:

http://www.godatabase.org/dev/java/dagedit/docs/index.html

To map your dataset to the GO slim terms, we provide a Perl script, 
map2slim, as part of the go-perl package:

http://www.geneontology.org/GO.slims.shtml#script

We're hoping to create a more user-friendly web-based application for 
mapping to GO slim terms, probably later this year.

Hope this helps - let us know if you need any further advice,

Jane Lomax
GO editorial office



On Tue, 17 May 2005, 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
> 
> 
> 
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