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looking for an expression analysis tool

Kara Dolinski kara at genomics.princeton.edu
Tue Jun 13 08:13:04 PDT 2006


Hello,

We have an implementation of the GO Term Finder at Princeton that  
should do the trick:

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

You can upload your own annotation file in the Advanced Options section.

Cheers,
Kara

On Jun 13, 2006, at 10:59 AM, Jane Lomax wrote:

> Hi Pascale - that's the sort of thing I'm after, but it looks like  
> GOAT takes the association files from the GO website, and doesn't a  
> user to
> upload their own ga file...
>
> Jane
>
> On Tue, 13 Jun 2006, Pascale Gaudet wrote:
>
>> Hi Jane,
>> I think that's what the GOAT tool from Qikai Xu and Gad Shaulsky does
>> http://dictygenome.bcm.tmc.edu/Downloads/GOAT/
>> "GOAT is a component of the microarray analysis tool package used  
>> in our lab to analyze Dictyostelium
>> discoideum expression data. It has been extended so that it can be  
>> used to analyze GO enrichment for
>> gene lists from any organism with genome-scale annotation data.  
>> GOAT is an R package with a Tk
>> graphical user interface (GUI), so it can be integrated into other  
>> R based microarray data analysis
>> packages such as BioConductor. "
>> Pascale
>> At 03:24 PM 6/13/2006 +0100, Jane Lomax wrote:
>>       Hi - does anyone devevelop, or know of, a gene expression  
>> analysis tool that uses GO, and
>>       allows a user to upload their own gene association file,  
>> preferably in standard GO format?
>>
>>       This is useful for species with no GO annotation in the GO  
>> database.
>>
>>       many thanks,
>>
>>       Jane
>>
>>       --
>>       Dr Jane Lomax
>>       GO Editorial Office
>>       EMBL-EBI
>>       Wellcome Trust Genome Campus
>>       Hinxton
>>       Cambridgeshire, UK
>>       CB10 1SD
>>
>>       p: +44 1223 492516
>>       f: +44 1223 494468
>>
>>       --
>>       This message is from the GOFriends moderated mailing list.   
>> A list of public
>>       announcements and discussion of the Gene Ontology (GO) project.
>>       Problems with the list?           E-mail: owner- 
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>> -- This message is from the GOFriends moderated mailing list. A  
>> list of public announcements and
>> discussion of the Gene Ontology (GO) project. Problems with the  
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>> owner-gofriends at geneontology.org Subscribing send "subscribe" to  
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>
> -- 
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468


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