[BioC] How to compare GO results

[Alex Sanchez]

Hi Johannes

There are several packages in BioC that you can use to do GO analysis or to 
mine GO analysis results.
You can find most, if not all, of them in the Bioconductor GO task view. 
(Curiously topGO is not there).

http://www.bioconductor.org/packages/release/GO.html

I am the maintainer of the 'goProfiles' package which is, in principle, 
developed to answer the type of question you pose.
If you have any questions about its use I'll be pleased to try to help you 
at answering them.

best

Alex Sánchez

...............................................................................................................
Dr. Alex  Sánchez.
Associate Professor. Statistics Department. University of Barcelona.
Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain
asanchez_at_ub.edu
Statistics and Bioinformatics Unit
Institut de Recerca. Hospital Universitari Vall 'Hebron
Passeig Vall d'Hebron 112-119. 08034 Barcelona
asanchez_at_ir.vhebron.net
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> Message: 17
> Date: Wed, 12 Aug 2009 09:10:56 +0200
> From: Johannes Hanson <s.j.hanson at uu.nl>
> Subject: [BioC] How to compare GO results
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <02C00589-9261-449C-B8A4-D7C8C4986E72 at uu.nl>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Dear all,
>
> This might not be a specific BioConductor question. However,
> BioConductor is my major tool and therefore I ask the question here.
> If not appropriate please ignore.
>
> I am analyzing array data from a set of mutants all showing the same
> phenotype. The idea was of course to find genes similarly expressed in
> all mutants to get closer to the regulatory mechanism of the phenotype.
> Surprisingly there was nearly no overlap among the differentially
> expressed genes. The suggestion was raised that the genes might encode
> similar functions. I therefore conducted GO analysis (using topGO and
> other packages). Still very little obvious overlap but how to quantify
> it? How to determine the degree of similarity between different GO
> results?
>
> All suggestions are welcome.
>
> Johannes Hanson
> Molecular Plant Physiology, Utrecht University
>
>
>