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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

GoName GoId top100 top300 top600 min p cutoff WRS p #genes
mitotic cell cycle 0000278 9e-05 5e-10 6e-07 3e-10 290 7e-08 93
M phase 0000279 1e-03 2e-06 1e-04 1e-09 1491 1e-07 41
nuclear division 0000280 1e-03 2e-06 1e-04 4e-09 1491 2e-07 40
M phase of mitotic cell cyc.. 0000087 6e-04 5e-07 1e-04 2e-08 1491 5e-07 36
mitosis 0007067 5e-04 4e-07 1e-04 6e-08 1491 1e-06 35
cell cycle 0007049 2e-04 3e-07 1e-05 1e-07 1571 6e-06 172
carbon-nitrogen ligase act.. 0016884 4e-04 3e-03 1e-02 3e-05 27 2e-05 2
carboxylic acid metabolism 0019752 9e-02 1e-04 4e-05 3e-06 711 3e-05 83
organic acid metabolism 0006082 9e-02 1e-04 4e-05 3e-06 711 3e-05 83
intramolecular isomerase .. 0016863 1e+00 3e-02 8e-04 2e-05 609 5e-05 4
cell proliferation 0008283 7e-04 2e-05 1e-03 4e-06 1956 8e-05 264
intramolecular isomerase .. 0016860 1e+00 2e-02 3e-03 3e-05 905 1e-04 9
spindle microtubule 0005876 4e-04 3e-03 1e-02 6e-05 42 1e-04 2
DNA replication and chro.. 0000067 6e-02 3e-04 2e-03 9e-05 852 3e-04 44
regulation of mitosis 0007088 9e-03 8e-03 5e-02 3e-04 1248 5e-04 8