Structural comparison of metabolic networks in selected single cell organisms

BMC Bioinformatics

Table 1 Descriptive statistics of metabolic networks in the eleven organisms.

DOMAIN, KINGDOM AND PHYLUM			ORGANISM	NUM NODES	NUM EDGES	SINGLE EDGES	MUTUAL EDGES	C_OUT	C_IN	B	L	D
Eukarya			S. cerevisiae	748	1072	396	338	0.066	0.062	0.053	12.147	49
Bacteria	Proteobacteria	gamma	E. coli	893	1365	459	453	0.060	0.070	0.070	9.281	30
			V. cholerae	738	1076	370	353	0.057	0.055	0.045	8.236	23
		beta	R. solanacearum	864	1238	406	416	0.044	0.044	0.049	10.358	43
	Firmicutes	Bacillales	B. subtilis	787	1151	401	375	0.061	0.063	0.047	10.020	29
		Lactobacillales	L. lactis	545	778	280	249	0.044	0.043	0.068	9.277	27
	Actinobacteria		S. coelicolor	814	1154	406	374	0.046	0.047	0.047	15.062	66
Archaea	Euryarchaeota		M. acetivorans	489	633	209	212	0.029	0.033	0.026	11.350	35
			T. acidophilum	458	593	197	198	0.034	0.036	0.030	10.597	33
	Crenarchaeota		S. solfataricus	586	730	256	237	0.022	0.021	0.018	8.053	26
			S. tokodaii	522	651	229	211	0.021	0.024	0.017	8.424	27

The column marked "Num nodes" lists the number of metabolites that are involved in at least one chemical reaction in the organism. The column marked "Num edges" lists the number of all directed chemical reactions in the organism. Note that this number consists of two parts: The number of irreversible reactions, i.e. "Single edges"; and the number of reversible reactions, i.e. "Mutual edges", where "Num edges" = "Single edges" + 2 × "Mutual edges". The column marked "C_out" lists the average clustering coefficient calculated from the nearest neighbors in out-component. The column marked "C_in" lists the average clustering coefficient calculated from the nearest neighbors in in-component. Column marked "B" lists the average betweenness of the network, the column "L" lists average path length of the network and column marked "D" lists diameter of the network.

ISSN: 1471-2105