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Jane Lomax jane at ebi.ac.uk
Mon Jul 11 03:38:43 PDT 2005


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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