Table 1.

Fractions of Consistent Transcription Factor Target Genes in the E. Coli 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
Motility	44	0.95	0.95	0.89	46	0.78	0.48	0.09	12	6	28	0	0
Flagellum	38	0.95	0.95	0.87	40	0.68	0.45	0.1	6	2	32	0	0
Nucleotide biosynthesis	18	0.83	0.83	0.72	18	0.5	0.11	0	16	0	2	0	0
Metabolism of other compounds	46	0.8	0.67	0.37	47	0.23	0.21	0	39	6	1	1	0
Cellular component biosynthesis	64	0.58	0.56	0.52	68	0.37	0.22	0.06	23	13	30	2	0
Chaperoning	28	0.57	0.57	0.39	30	0.3	0.13	0.03	17	7	3	3	0
Posttranscriptional regulation	17	0.53	0.53	0.35	19	0.37	0.21	0	12	5	1	0	1
Primary active transporters	94	0.51	0.41	0.28	95	0.14	0.07	0	62	16	0	4	13
Group translocators	16	0.38	0.38	0.38	17	0.35	0.18	0	5	5	7	0	0
Macromolecule degradation	14	0.36	0.36	0.29	15	0.07	0	0	10	4	1	0	0
Membrane components	172	0.34	0.32	0.23	186	0.14	0.08	0.01	86	52	18	14	16
Central intermediary metabolism	91	0.34	0.26	0.14	99	0.07	0.03	0	42	26	10	14	7
Energy metabolism	93	0.33	0.3	0.22	102	0.06	0.03	0	27	22	7	23	23
Carbon compound utilization	115	0.33	0.29	0.22	126	0.18	0.1	0	47	52	20	6	1
Amino acid biosynthesis	66	0.33	0.27	0.17	74	0.09	0.03	0	56	8	5	4	1
Energy production/transport	55	0.31	0.27	0.15	56	0.04	0.02	0	10	18	4	11	13
Adaptation to stress	37	0.27	0.22	0.14	46	0.11	0.09	0	31	7	6	2	0
Transcriptional regulation	42	0.26	0.24	0.12	63	0.1	0.08	0	36	15	5	6	1
Amino acid utilization	22	0.23	0.23	0.14	27	0.11	0.07	0	14	4	0	3	6
Transcription	40	0.23	0.2	0.1	60	0.08	0.07	0	36	13	4	6	1
Cofactor biosynthesis	28	0.18	0.18	0.07	30	0.03	0.03	0	24	4	2	0	0
EC potential driven transporters	36	0.17	0.11	0.08	42	0.12	0.07	0.02	17	15	4	4	2
Cell protection	25	0.08	0.08	0	31	0.19	0.03	0	24	5	1	0	1

The functional classes were obtained from the GenProtEC database (Serres and Riley 2000). Only functional classes with at least 15 genes in the network are included. Results considering both multiregulator modules (MRM) and target modules (TM) are shown. n, number of targets in this class (for MRMs this is the number of targets in this class participating in MRMs with more than one target). Fractions of consistent targets in a particular class at particular P-value cutoffs are shown. The number of regulator columns show the number of target genes in a functional class with the indicated number of regulators.

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