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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
>>>
>>> --
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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
--
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Problems with the list? E-mail: owner-gofriends at geneontology.org
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