Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?
I have tried the following:
Batch tool for GSFS: PROBLEM: It says that my input yeast genes are not human genes (which probably means that the tool will work only with Human genes).
http://bioinformatics.clemson.edu/G-SESAME/Program/geneCompareTwo1.php : PROBLEM: provides score for every gene pair input. I have ~3600 genes. Impossible to do it for eveyr pair.
DAVID batch viewer gives a 1xN matrix (functional similarity score of one gene to a set of N genes, when I want all possible pairs of similarities which will give an NxN matrix)
GO funsimmat- I am unable to get this to work, so I'm not sure if it will give me the desied results.
GO FastSemSim- same as 4.