Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments

Table 3 Number of significant Gene Ontology categories and assigned genes among methods for Nickel exposure dataset

		Number of unique genes				Number of significant categories
p -value	Time pt	T	FOLD	SMT	IBMT	T	FOLD	SMT	IBMT
0.0001	03 hr	0	0	0	0	0	0	0	0
0.001	03 hr	0	0	0	0	0	0	0	0
0.005	03 hr	4	6	6	8	2	3	3	4
0.0001	08 hr	0	16	0	46	0	1	0	2
0.001	08 hr	0	49	12	54	0	5	9	12
0.005	08 hr	14	71	53	54	6	28	21	20
0.0001	24 hr	25	22	26	26	11	15	15	15
0.001	24 hr	52	32	62	56	15	19	21	19
0.005	24 hr	65	66	72	69	25	34	35	35
0.0001	48 hr	0	0	42	46	0	0	1	2
0.001	48 hr	2	9	44	52	1	3	4	6
0.005	48 hr	49	34	49	60	8	26	15	25
0.0001	72 hr	0	59	57	58	0	9	5	7
0.001	72 hr	45	61	63	66	3	17	12	11
0.005	72 hr	51	68	77	71	7	42	20	17
	Total	307	493	563	666	78	202	161	175
	# Zeroes	6	3	3	2
	# Best	0	2	4	8	0	6	3	7

The number of significant categories, as well as the number of genes assigned to the significant categories, are shown for the five time points for each of three p-value cut-offs.

ISSN: 1471-2105