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.

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