Table 1 Results for GRP 2 (NKI data) for three signatures. Top: Pei. Middle: Chang. Bottom: Wong–Mitochon. The p-values have been Bonferroni corrected.

Hierachy level	Genes removed	Cum. sum of genes removed	Genes left	GO-terms removed	Cum. sum of GO-terms removed	Acc. (%)	Sig.Acc. (%)
16	3	3	12,135	1	1	3.3	2.5
15	8	11	12,127	3	4	4.0
14	2	13	12,125	1	5	2.9
13	177	190	11,948	2	7	4.7
12	1318	1508	10,630	9	16	3.3
11	616	2124	10,014	8	24	3.7
10	432	2556	9582	10	34	3.2
9	229	2785	9353	11	45	3.4
8	190	2975	9163	13	58	3.1
7	197	3172	8966	9	67	2.8
6	533	3705	8433	24	91	2.5
5	854	4559	7579	16	107	3.2
4	837	5396	6742	4	111	4.1
3	130	5526	6612	4	115	2.5
2	250	5776	6362	3	118	3.0
1	56	5832	6306	1	119	3.2
18	17	17	11,822	1	1	87.0	88.5
17	11	28	11,811	3	4	87.9
16	3	31	11,808	2	6	89.6
15	89	120	11,719	8	14	89.2
14	203	323	11,516	24	38	89.8
13	819	1142	10,697	41	79	87.4
12	1932	3074	8765	91	170	87.1
11	1246	4320	7519	112	282	84.8
10	1216	5536	6303	153	435	84.3
9	1326	6862	4977	174	609	81.9
8	1252	8114	3725	183	792	79.6
7	1258	9372	2467	193	985	70.8
6	711	10,083	1756	165	1150	81.2
5	573	10,656	1183	97	1247	73.2
4	336	10,992	847	54	1301	88.1
3	122	11,114	725	27	1328	86.3
18	17	17	11,913	1	1	78.9	78.0
17	9	26	11,904	3	4	74.9
14	63	89	11,841	9	13	76.7
13	228	317	11,613	12	25	78.0
12	1228	1545	10,385	25	50	78.7
11	826	2371	9559	53	103	76.3
10	1054	3425	8505	60	163	75.5
9	1032	4457	7473	70	233	76.8
8	949	5406	6524	77	310	78.6
7	1754	7160	4770	89	399	69.7
6	810	7970	3960	78	477	68.6
5	868	8838	3092	67	544	63.4
4	461	9299	2631	35	579	63.6
3	339	9638	2292	24	603	65.6
2	238	9876	2054	12	615	56.0
1	30	9906	2024	3	618	56.6

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