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[gofriends] GO visualisation tool?

Jim Hu jimhu at tamu.edu
Thu Jan 10 08:24:40 PST 2008


Hi Rachael,

On Jan 10, 2008, at 10:00 AM, Rachael Huntley wrote:

> Hi Jim,
>
> He has done a microarray experiment and wants to cluster the genes  
> according to GO, so he wants to see the GO tree with the genes  
> displayed under the GO terms they are annotated to. I don't think  
> AmiGO does this sort of thing.

Ah, that makes sense.  So, if I understand this right, a general tool  
would be something where you give a program the ontology, a gene  
association file, and a list of genes, and get the appropriate  
display.  This has to be filtered for statistically enriched  
associations to be useful, I think.  I'm interested to see what others  
suggest.  I think that various projects have their own organism- 
specific versions of this, and I think it's built into commercial  
packages like GeneSpring.  But I'd like to see a list and discussion  
of what's available as open source... especially for things that can  
be displayed as web tools.

Jim

>
>
> Rachael.
>
> Jim Hu wrote:
>
>> Hi Rachael,
>>
>> I'm not sure I understand what the user wants to do.  Doesn't AmiGO  
>> place genes under the appropriate branches based on annotations?   
>> Is this not the desired kind of visualization?  Or do they want  
>> something different?
>>
>> Jim
>>
>>
>> On Jan 10, 2008, at 7:46 AM, Rachael Huntley wrote:
>>
>>> Dear all,
>>>
>>> I have had this query from a user, does anyone know of a tool that  
>>> can do this?
>>>
>>> >Do you know of any GO viewer that allows you to visualise the  GO  
>>> structure and place genes with a specific annotation under that   
>>> branch of the tree?
>>> <
>>>
>>> Thanks,
>>> Rachael.
>>>
>>> -- 
>>> Rachael Huntley Ph.D.
>>>
>>> European Bioinformatics Institute-EMBL
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom  Tel: +44 (0)1223 492515
>>> Fax: +44 (0)1223 494468
>>>
>>> E-mail: huntley at ebi.ac.uk <mailto:huntley at ebi.ac.uk>
>>> URL: http://www.ebi.ac.uk/GOA
>>>
>>>
>>> --
>>> This message is from the GOFriends moderated mailing list.  A list  
>>> of public
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>>> Web:          http://www.geneontology.org/
>>
>>
>> =====================================
>>
>> Jim Hu
>>
>> Associate Professor
>>
>> Dept. of Biochemistry and Biophysics
>>
>> 2128 TAMU
>>
>> Texas A&M Univ.
>>
>> College Station, TX 77843-2128
>>
>> 979-862-4054
>>
>>
>>
>
>
> -- 
>
> Do you need any additional GO annotation resources?
> Which proteins would you like annotated with GO?
>
> Let us know in the GOA User Survey, available at http://www.ebi.ac.uk/GOA/contactus.html
>
>
> *************************************
>
> Rachael Huntley Ph.D.
>
> European Bioinformatics Institute-EMBL
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 492515
> Fax: +44 (0)1223 494468
>
> E-mail: huntley at ebi.ac.uk
> URL: http://www.ebi.ac.uk/GOA
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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