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[Gofriends] Need a software to map GO annotation

Sorin Draghici sorin at wayne.edu
Mon Sep 28 19:44:21 PDT 2009


Erika,

Onto-Express to go (OE2GO) allows you to upload any custom
annotations. Once you have uploaded them you can do any GO
enrichment/depletion analysis. The results are displayed as a list of
GO terms that can be sorted by p-values, etc. but also as a graphical
tree. The DAG links are not shown as in AmiGO but as in a tree. The
nodes with more than one parent can be reached from any parent. A
search for a node with more than one parent will automatically expand
all parents necessary showing all the paths from the root to the
searched term.

OE2GO is described in the following paper:
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1933142&blobtype=pdf

You can try the visualization capabilities using, Onto-Express, the
on-line tool that does the same things.

http://vortex.cs.wayne.edu

You can use some of the sample data sets we have on-line to see if the
capabilities are what you need.

All the best,

Sorin



> 
> On Sep 28, 2009, at 3:46 AM, Erika Feltrin wrote:
> 
>> Dear all,
>>
>> I am working on the grape annotation project and in particular on the GO
>> annotation of grape genes/proteins.
>> Currently I have a list of genes annotated to GO vocabularies and I
>> would like to visualize these genes on the DAG GO structure like AmiGO
>> does.
>> The file has a column with the grape gene ID and a column with the GO
>> ID.
>> I do not find any tool with this function. Does anybody know if there is
>> a software that allows to map custom GO annotation of a non-consortium
>> organism to the GO DAG graph?
>>
>> Thanks
>> Erika
>>
>>
>> -- 
>> ********************************
>> Erika Feltrin, PhDwould 
>> Bioinformatics Lab
>> CRIBI-Padua University
>> Viale G. Colombo, 3
>> 35121 Padova-Italy
>>
>> http://genomics.cribi.unipd.it
>> Phone. +39. 049 827-6165
>> Fax.   +39. 049 827-6159
>> ********************************
>>
>> _______________________________________________
>> Gofriends mailing list
>> Gofriends at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/gofriends
> 
> =====================================
> 
> 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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> Gofriends at geneontology.org
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-- 

Associate Professor
Director of the Intelligent Systems and Bioinformatics Laboratory
Department of Computer Science
Wayne State University
Room 431 State Hall,
5143 Cass Ave,
Detroit, MI 48202
Tel: 313-577-5484
Fax: 313-577-6868
http://vortex.cs.wayne.edu




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