Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[gofriends] GO visualisation tool?

Vivian Lee vlee at ebi.ac.uk
Thu Jan 10 09:04:15 PST 2008


Hi Rachael and Jim,

Ive been asked the same question when I was in a conference giving the GOA
presentation. I am sure that a number of the tools at GO consortium
website (http://www.geneontology.org/GO.tools.microarray.shtml) will do
the visualization in addition to statistic analysis/annotation. I have got
a recommendation from a friend who used gosurfer
(http://bioinformatics.bioen.uiuc.edu/gosurfer/applications.htm) to
present their microarray data with the GO tree pic which then was
published in a journal (Mol Psychiatry. 2004 Jul;9(7):684-97, 643.) Also
heard that some tools provide options of colour scheme and shape of
nodes:-) (so you can personalise the layout).
It is worthy noting that using a tool with regular updates of GO
annotation will give a better result.
Hope this helps.

Vivian


> 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>
>>>> Subscribing   send   "subscribe"   to
>>>> gofriends-request at geneontology.org
>>>>  <mailto:gofriends-request at geneontology.org>
>>>> Unsubscribing send   "unsubscribe"  to
>>>> gofriends-request at geneontology.org
>>>>  <mailto:gofriends-request at geneontology.org>
>>>> 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
>> 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
>
>
>



--
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
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list