Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP

Table 2 Size of the functional similarity networks.

Organism	Number of Nodes ^a)	Functional Similarity Category	Number of Nodes with 2+ Edges ^b)/Edges
			0.80 ^c)	0.95	0.99
E. coli K-12	4169	BP	3085/208664	2169/44063	1497/13893
		CC	1603/584156	600/19862	425/17252
		MF	3033/321422	2161/74164	998/9576
		funSim	2901/121999	1172/7003	414/2648
S. cerevisiae	6428	BP	4622/253711	4070/72191	3270/33282
		CC	4442/3246553	2717/113947	2208/83648
		MF	4293/826942	3246/87173	1871/14257
		funSim	3879/48115	1755/10679	954/5431
P. falciparum	4784	BP	3968/1730159	2356/50180	1346/18444
		CC	1696/443757	1201/19154	1021/9524
		MF	4057/2619387	3788/1658678	1098/9977
		funSim	4002/208085	1521/14075	536/3134

a) The number of proteins which have annotated function or high confident predicted function (the last column in Table 1).
b) The number of proteins (nodes) which have at least two edges so that the clustering coefficient can be computed.
c) The threshold value of the functional similarity score to connect an edge between pairs of nodes.

ISSN: 1471-2105