Table 3.

Conservation of yeast protein interactions

	P(Fly)	P(Fly|HPD)	P(Worm)	P(worm|HPD)
Yeast	0.020 (10/409)	0.051 (4/79)	0.004 (2/457)	0.027 (2/75)
Yeast-large	0.009 (56/6113)	0.061 (34/559)	0.001 (3/5823)	0.005 (3/547)

We consider a protein interaction in yeast to be conserved in another organism if both interacting proteins in yeast have orthologs in the other organism, and the orthologous proteins interact. P(Fly) and P(Worm), probability of a protein interaction in a S. cerevisiae PIN to be conserved in Fly and Worm, respectively. P(Fly|HPD) and P(Worm|HPD), probability of a protein interaction in a S. cerevisiae PIN to be conserved in fly and worm given that it is a homomeric interaction or an interaction between paralogous proteins.