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[gofriends] GO visualisation tool?

Marc Gillespie gillespm at cshl.edu
Thu Jan 10 08:35:53 PST 2008


Hi All,

I wasn't going to post back (laziness?), but your unabashed interest  
got me started. We have been looking at DAVID to get students going on  
microarray work, it is free, it parses microarray data, and it seems  
to have a nice GO term clustering facility.

I haven't delved into it yet, but will in about two months, when I  
have to write up a formal microarray lab for undergrads.

Hope this helps,

Marc


Marc Gillespie Ph.D.
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724   USA

Office (718) 990-5249

email gillespm at cshl.edu




On Jan 10, 2008, at 11:24 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
>>>> announcements and discussion of the Gene Ontology (GO) project.
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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
>
>

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