[BioC] How to compare GO results

[Johannes Hanson]

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