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looking for an expression analysis tool

Jane Lomax jane at ebi.ac.uk
Tue Jun 13 08:18:43 PDT 2006


Hi Kara - yes, I've looked at your tool and it is excellent, but what I 
need for these purposes is something that also provides some sort of
statistical analysis of over-representation of GO terms within a gene set, 
which the user uploads - sorry, wasn't very clear there.

thanks,

Jane

On Tue, 13 Jun 2006, Kara Dolinski wrote:

> 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.
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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
>
>
> --
> 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-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/

-- 
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-gofriends at geneontology.org
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