GENPPI: standalone software for creating protein interaction networks from genomes

BMC Bioinformatics

Table 1 Sample of model organisms obtained from the STRING database according to seven network metrics

Organism	STRING nomenclature	Vertices	Average degree	Density	Edges	Maximum degree
Escherichia coli	ATCC 8739	4190	195.34	0.047	409,238	1697
Bacillus subtilis	subsp. subtillis	4181	244.388	0.058	51,0983	2014
Caulobacter crescentus	CB15	3721	208.14	0.056	387,245	1393
Mycoplasma genitalium	ATCC 33530	474	128.35	0.271	30,419	318
Synechocystis (Cyanobacteria)	sp. ATCC 27150	4124	215.33	0.052	444,011	1548
Pseudomonas fluorescens	NCIMB 11764	6384	247.91	0.039	791,330	2158
Azotobacter vinelandii	DJ	4955	233.558	0.047	578,640	2047
Streptomyces coelicolor	A3(2)	7741	357.142	0.046	1,382,317	3576

We define these networks as appropriate to infer centrality measures. The majority of the networks from this sample have densities less than 0.100. The average degree, density, and edges were 228, 0.077, and 567 thousand, respectively

ISSN: 1471-2105