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

Table 4 Enrichment of function annotation to subnetworks.

Organism	# of subnetworks	# of edges	# of edges with common annotation ^a)	# of edges with common annotation or prediction ^b)	# of edges with common predicted annotation ^c)	# of subnetworks with functionally enriched edges ^d)
E. coli	632	6401	2689 (42.0%)	2718 (42.5%)	29 (0.5%)	17
S. cerevisiae	1148	38108	29407 (77.2%)	29407 (77.2%)	0 (0%)	0
P. falciparum	155	2578	241 (9.3%)	972 (37.7%)	731 (28.4%)	131

a) Edges connecting two nodes with (at least one) common GO annotation in the GOA database. In the parentheses, the fraction of the edges relative to the total number of edges is shown.
b) Edges connecting two nodes with (at least one) common annotation in the GOA database or common GO term prediction by PFP.
c) Edges connecting two nodes with common GO term prediction by PFP.
d) Subnetworks where the number of edges with common annotation increased by considering PFP prediction.

ISSN: 1471-2105