Table 1 Category p-values for cutoff-based and cutoff independent score functions. The 15 GO categories with the lowest Wilcoxon rank sum p-values from the ranked gene list, based on the data set of van't Veer et al., which comprises 5224 genes in total. Three columns show p-values for cutoff based score functions, with cutoffs at position 100, 300 and 600 in the list. The columns "min p" and "cutoff" give the minimal cutoff based p-value and the cutoff where this minimum was attained. The column "WRS" gives the p-value calculated with the Wilcoxon rank sum as score function and random permutation of genes as null hypothesis, and the column marked #genes indicates the total number of genes in the category. A full table (sorted by WRS p-value) is given as supplementary information [see Additional file 2]. The supplementary table also contains the ranking of each category using the different methods and the 25th, 50th and 75th percentiles of those genes in the ranked list.

From: Comparing functional annotation analyses with Catmap