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[gofriends] GO visualisation tool?

Ana Conesa aconesa at cipf.es
Fri Jan 11 07:39:48 PST 2008


Blast2GO is a free available tool (http://www.blast2go.org) that does 
exactly that. You can upload  your GO annotation file (or generate it  
with the tool), select the genes you want to visualize and using the 
"Combined Graph" functionality create the corresponding DAG. Seeing the 
genes annotated at the GO term is an option of the Combined Graph function.
Besides this, B2G also makes enrichment analysis, so you can visualize 
and highlight only enriched terms.
Blast2GO is a desktop application you can download and run form your 
computer. We are now working on the integration of this tool within the 
Babelomics suite (http://www.babelomics.org), which will be available 
very soon on the web.  Babelomics has a wide repertoire of statistical 
methods for functional analysis. This integration will provide an 
annotation and a high performance visualization engines to the 
Babelomics suite.

Ana



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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>>>> Unsubscribing send   "unsubscribe"  to 
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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 <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
>
>
>


-- 
------------------------------------------
Ana Conesa, PhD
Bioinformatics Department
Centro de Investigaci—n Pr’ncipe Felipe
Avda. Autopista Saler, 16
46013 Valencia Spain
http://bioinfo.cipf.es/aconesa
==========================================
CAMDA2007 Conference @ CIPF
http://camda.bioinfo.cipf.es
==========================================

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