A speed comparison of the tools reviewed here. Four sets of 100, 200, 500 and 1000 human genes were submitted to each tool. The three fastest tools, GoSurfer, GeneMerge and Onto-Express, are all able to perform the analysis of up to 200 genes in under 8 seconds. Note that GOTM allows upload of only up to 500 genes.

Reference:
Purvesh Khatri and Sorin Draghici. Ontological analysis of gene expression data: current tools, limitations, and open problems. 
Bioinformatics (2005) 21: 3587-3595