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[gofriends] GO visualisation tool?

Martha Arnaud arnaudm at genome.Stanford.EDU
Thu Jan 10 08:49:14 PST 2008


Hi Jim, Rachael--

> 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.

How about GO Term Finder?  The folks at Princeton have a nice, very  
flexible implementation of it available on their web site:
http://go.princeton.edu/cgi-bin/GOTermFinder
You can try it out with the list of S. cerevisiae genes they provide  
(the "SGD sample gene list").  Scroll down the results page to see  
the graph; it is displayed below the results table.

It's open source; see
http://www.ncbi.nlm.nih.gov/pubmed/15297299?dopt=Abstract

Martha

On Jan 10, 2008, at 8:24 AM, 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
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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
>> 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
>
>

**********************************************************
Martha B. Arnaud, Ph.D.
Senior Scientific Curator, Candida Genome Database
Department of Genetics
Stanford University School of Medicine
Stanford, CA 94305-5120
arnaudm at genome.stanford.edu
http://www.candidagenome.org
********************************************************** 
  
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