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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
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.
Hope this helps you out,
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
> papers are made using GO slims, which are basically cut-down versions
> the GO, containing usually just a small number of high-level GO terms.
> provide a generic GO slim and some species-specific slims here:
> Or you could create your own using the ontology editor DAG-Edit:
> To map your dataset to the GO slim terms, we provide a Perl script,
> map2slim, as part of the go-perl package:
> 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:
>> 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
>> put generate a graphical pie chart showing the percentages of high
>> level GO
>> terms aligning with that cluster? Several genome annotation papers
>> this type of output; however I'm not sure if there is a program that
>> generates this type of display.
>> Nathan Salomonis
>> University of California, San Francisco
>> Pharmaceutical Sciences and Pharmacogenomics
>> GenMAPP (Gene Map Annotator and Pathway Profiler)
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