[gofriends] GO visualisation tool?

[Sorin Draghici]

Hi,

A list of such tools together with an extensive discussion is available in:

Purvesh Khatri and Sorin Draghici. Ontological analysis of gene expression data:
current tools, limitations, and open problems. Bioinformatics, 21(18):3587-95,
September 2005.

The paper is available here:

http://vortex.cs.wayne.edu/papers/Ontological_analysis.pdf


Regards,


Sorin Draghici, Ph.D.


Director of the Bioinformatics Core, Karmanos Cancer Institute

Associate Professor		Tel: (313) 577-5484
Dept. of Computer Science	Fax: (313) 577-6868
Wayne State University
5143 Cass Ave, Room 431 State Hall,
Detroit, MI, 48202
WWW: http://vortex.cs.wayne.edu/Sorin/index.htm (personal)
WWW: http://vortex.cs.wayne.edu/Projects.htm (lab)


Check out my recent book: Data Analysis Tools for Microarrays:
http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc=



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
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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
> 
> 
> 

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