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Kara Dolinski kara at genomics.princeton.edu
Mon Jul 11 06:01:37 PDT 2005


Hi,

We have implemented a version of the GO Term Finder (see Boyle et al 
Bioinformatics. 2004 Dec 12;20(18):3710-5) that works for Dicty (and 
any other species for which a GO annotation file is provided via the GO 
consortium site).  The URL is:

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

I think this might do the trick for you.

Cheers,
Kara

On Jul 11, 2005, at 6:38 AM, Jane Lomax wrote:

> Hi Alessio,
>
> That's actually a really good point. There are a large number of these
> sort of tools (Sorin's paper reviewed just 15 of them) but they tend to
> only cover human, and the major model organisms such as Drosophila and
> mouse.
>
> The tools for expression analysis using GO are listed at:
>
> http://www.geneontology.org/GO.tools.microarray.shtml
>
> but from a quick scan, I couldn't see any that cater for Dicty. Do 
> people
> know of any?
>
> thanks,
>
> Jane
>
> On Fri, 8 Jul 2005, Alessio Sillo wrote:
>
>>
>> Dear Go friends,
>>
>> I write You because I have performed a microarray experiment using
>> Dictyostelium discoideum as experimental model.
>> After having calculated the statistics to select only significant
>> differentially expressed genes I would like to use GO annotations to
>> arrange my list of genes into groups.
>> I would like to do with Dicty genes what EASE
>> (www.geneontology.org/GO.tools.microarray.shtml#ease) does with human
>> genes, that is summarizing the predominant biological "theme" of a 
>> given
>> gene list. Given a list of genes resulting from a microarray or other
>> genome-scale experiment, EASE can rapidly calculate 
>> over-representation
>> statistics for every possible Gene Ontology term with respect to all 
>> genes
>> represented in the data set.
>>
>> However, I have appreciated that the AmiGO gene ontology classifies 
>> Dicty
>> genes as well by biological process, molecular function and cellular
>> component.
>> How can I make a query in AmiGO with my list of differentially 
>> expressed
>> genes? Is there a query webpage where I can put my list of genes and 
>> I can
>> get them arranged in functional groups?
>>
>> I look forward to hearing from You.
>>
>> I will accept any suggestion with pleasure and gratitude.
>>
>> Thanks a lot,
>>
>>
>> Alessio Sillo
>> Cell Biology Laboratory
>> Dept. Clinical and Biological Sciences
>> University of Torino
>> Italy
>>
>> --
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>
>
>
>
> --
> This message is from the GOFriends moderated mailing list.  A list of 
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