Table 2 Comparison of different cutoff independent approaches. The top ten categories and their corresponding ranks for each of the the four methods: Wilcoxon rank sum (WRS) with sample label permutation null hypothesis (s.l.p.), WRS with gene permutation null hypothesis (g.p.), the Kolmogorov-Smirnov score (K-S) as used in GSEA [17], and the minimal cutoff-based p-value (min-p) [7, 8]. Percentile columns indicate the position of the 25th, 50th and 75th percentile in the ranked gene list which comprises 5224 genes and is based on the data set of van't Veer et al.. The last column indicates the number of genes in each category. The full table is available as a supplementary file [see Additional file 3].

From: Comparing functional annotation analyses with Catmap