Running time as function of the significance value. A: For a sorted list of 1000 genes and a category containing 100 genes the runtime of our algorithm was computed for a set of discrete p-values (0, 0.003, 0.006,...,0.996, 1). The shown runtime is the median of 100 runs for each p-value on a standard 2 GHz PC. The maximal runtime was 0.05 seconds spent for computing the complete matrix. A naive permutation test procedure needed about 0.7 seconds for 1000 permutations. B: Running time as function of the significance value for small p-values.