The results of mummichog method from Functional Analysis module consists of the total number of hits, the raw p-value (Fisher’s), the Gamma-adjusted p-value (for permutations), and the Empirical p-value per pathway.
The Gamma-adjusted p-values are the Fisher’s p-values calculated using Lsig that are adjusted for the null distribution of permutation p-values.
Meanwhile, the Empirical p-values consist of the number of times the p-values using the permuted data were better than the p-values using the significant data, divided by the number of permutations.