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[gofriends] GO visualisation tool?

Peter Robinson peter.robinson at charite.de
Thu Jan 10 08:48:11 PST 2008


I am not sure I understand the requirement, but The Ontologizer provides 
a visualization of significant terms and their anscestors within the 
Ontology. Users can click on each term to display a list of all genes 
annotated (directly or by inheritance) to the term within the table 
browser.

http://www.charite.de/ch/medgen/ontologizer


Depending on the analysis being done, it is unlikely to be helpful to 
actually display the lists of genes in the graphic itself because of 
information overload.

Take care, Peter



Jim Hu wrote:
> 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
>>>> announcements and discussion of the Gene Ontology (GO) project.
>>>> Problems with the list?           E-mail: 
>>>> owner-gofriends at geneontology.org 
>>>> <mailto:owner-gofriends at geneontology.org>
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>>>
>>>
>>> =====================================
>>>
>>> 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 <mailto: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
> 
> 
> 


-- 
Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik
Universitätsklinikum Charite
Humboldt-Universität
Augustenburger Platz 1
13353 Berlin
Germany
voice: 49-30-450569124
fax:   49-30-450569915
email: peter.robinson at charite.de
http://www.charite.de/ch/medgen/robinson

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