Regulatory network operations in the Pathway Tools software

BMC Bioinformatics

Table 2 Selected statistics on regulation data content for several organisms

	*E. coli* K-12	*B. subtilis*	*S. oneidensis*	*Shewanella* sp.	*Synechococcus*
	MG1655	*subtilis* 168	MR1	W3-18-1	sp. PCC7002
Transcriptional regulation	3118	781	589	569	114
Transcription factor binding	3032	747	589	569	114
Allosteric regulation of RNA-polymerase	66	0	0	0	0
Attenuation	20	34	0	0	0
Translational regulation	97	5	0	0	4
Protein-mediated	31	2	0	0	0
RNA-mediated	59	1	0	0	0
Small-molecule-mediated	5	2	0	0	4
Enzyme modulation	2508	9	0	0	5
Physiologically relevant	210	2	0	0	2
Genes with ≥ 1 transcriptional/translational regulator	1771	1087	542	539	124
Percent of genome	39%	25%	12%	13%	4%
Transcriptional or translational regulators	260	151	62	54	19
Proteins	225	128	62	54	16
RNAs	27	15	0	0	0
Small molecules	8	8	0	0	3
Enzymes subject to modulation	597	8	0	0	3
Physiologically relevant^a	114	1			1
Enzyme modulators	1016	6	0	0	5
Physiologically relevant^a	108	2			2

^aFor enzyme modulation, a distinction is made between physiologically relevant effects and those that have been observed purely in vitro.

ISSN: 1471-2105