Table 2.

Fractions of Consistent Transcription Factor Target Genes in the Yeast Regulatory Network Classified by the Functional Class of the Target

	MRM							TM
Functional class	n	P < 0.01	P < 0.005	P < 0.001	n	P < 0.01	P < 0.005	P < 0.001	1	2	3	4	>4
Pheromone response	10	0.4	0.4	0.3	30	0.37	0.27	0.13	6	8	5	3	8
Detoxification	16	0.38	0.38	0.31	27	0.33	0.22	0.07	11	10	4	0	2
Nucleotide metabolism	21	0.33	0.24	0.19	25	0.28	0.2	0.2	3	16	3	3	0
DNA synthesis and replication	11	0.27	0.27	0.18	18	0.17	0.06	0	8	6	2	1	1
Amino acid metabolism	35	0.26	0.2	0.11	61	0.39	0.33	0.18	23	14	16	5	3
Carbohydrate metabolism	50	0.26	0.18	0.12	83	0.2	0.13	0.06	26	22	20	3	12
Mitotic cell cycle and cell cycle control	27	0.22	0.22	0.19	43	0.14	0.14	0.02	18	14	5	1	5
Nitrogen and sulfur metabolism	14	0.14	0.14	0.07	28	0.39	0.39	0.32	5	9	6	6	2
Cellular import	18	0.11	0.11	0.06	21	0.29	0.29	0.14	5	9	5	2	0
Stress response	18	0.11	0.11	0.11	29	0.1	0.07	0.07	12	8	5	1	3
Meiosis	20	0.1	0.1	0.1	26	0.04	0.04	0	12	7	2	1	4
mRNA synthesis	34	0.06	0.06	0.03	64	0.16	0.11	0.06	30	18	6	1	9
Lipid, fatty-acid and isoprenoid metabolism	30	0.03	0.03	0.03	39	0.13	0.13	0.05	20	8	5	4	2
DNA recombination and DNA repair	11	0	0	0	19	0.05	0.05	0	10	4	3	1	1
Sporulation and germination	8	0	0	0	17	0.12	0.06	0	5	6	2	2	2

See caption for Table 1 for details. The functional classes were obtained from the MIPS database (Mewes et al. 2002).

Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures