Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes

Table 1 Statistics of the PINs from five eukaryote species

Species	Dataset	Data type	n ^a	#of links	ν ^b	<k>^c	*<C>* ^d	r ^e	*<L>* ^f	M ^g
Yeast	MIPS	Manually curated	3,891	7,270	0.47***	3.74	0.066	-0.14***	4.85	0.662
	Yu et al. (2008)	Y2H	1,647	2,518	0.25***	3.06	0.057	-0.11***	5.61	0.739
	Batada et al. (2007)	Multi-Validated	3,801	9,742	0.33***	5.13	0.171	-0.12***	4.69	0.715
	Reguly et al. (2006)	Literature curated	3,224	11,291	0.33***	7.00	0.266	-0.13***	4.22	0.689
Worm	Li et al. (2004)	Y2H	2,898	5,240	0.29***	3.62	0.072	-0.14***	4.95	0.679
Fly	Pacifico et al. (2006)	Y2H	2,477	3,546	0.35***	2.87	0.025	-0.09***	5.93	0.738
Human	Rual et al. (2005)	Y2H, Literature Curated	2,783	6,007	0.26***	4.32	0.072	-0.14***	4.84	0.630
	Stelzl et al. (2005)	Y2H	1,613	3,101	0.27***	3.85	0.006	-0.20***	4.85	0.588
Malaria parasite	LaCount et al. (2005)	Y2H	1,267	2,726	0.02	4.30	0.014	-0.03*	4.26	0.506

a. Number of nodes in a network.
b. The extent of disassortative structure. *** indicates a significantly non-zero value (P < 0.001).
c. The mean degree.
d. The mean cluster coefficient. The cluster coefficient of node i is defined as C_i = 2e_i/k_i(k_i-1), where k_i is the degree of node i and e_i is the number of links connecting k_i neighbors of node i to one another [67]. When k_i is one, C_i is defined to be zero. C_i is equal to one when all neighbors of node i are fully connected to one another, while C_i is zero when none of the neighbors are connected to one another.
e. The Pearson correlation coefficient between degrees of two nodes connected to each other. *, P < 0.05; **, P < 0.01; ***, P < 0.001.
f. The mean shortest path length, which is defined as the mean of the shortest path length between all pairs of nodes in a network [14].
g. The modularity. See Methods.

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