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Pie Chart view of Gene Ontology percentages

John C. Matese jcmatese at genomics.princeton.edu
Wed May 18 05:27:45 PDT 2005


Hi Nathan,

Regarding the web-enabled GO slim concept that Jane mentioned, the 
group here at Princeton (primarily Linda McMahan) crafted a webtool 
version of map2slim (Chris Mungall), that allows uploaded genelists 
with a chosen slim-file from the GO consortium site.  It doesn't export 
pie-chart currently, but the data it produces may be helpful to you.

http://go.princeton.edu/cgi-bin/GOTermMapper

Hope this helps you out,

John Matese





On May 18, 2005, at 6:13 AM, Jane Lomax wrote:

> 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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