Table 1. Number of proteins and their interactions in each connected component of the yeast interaction network.

connected component	yeast protein interaction network		node degree
	# nodes	# edges	average	maximum	minimum
0	3,736	13,765	7	255	1
1	3	2	1	2	1
2	2	2	1	2	1
3	2	1	1	1	1
4	2	2	1	2	1
5	2	2	1	2	1
6	2	1	1	1	1
7	2	2	1	2	1
total	3,751	13,777	7	255	1

Table 2. Number of yeast proteins matched to human proteins. The total number of yeast proteins matched to human proteins is 1,934.

	Yeast proteins	Human proteins
	9	1
	8	1
	7	3
	6	3
	5	10
	4	52
	3	175
	2	1,476
	1	9,876
total		11,597

Table 3. Number of proteins and their interactions in each of the 14 connected component of the human interaction network, derived from yeast protein interactions.

conn. comp.	human protein interaction network		node degree
	# nodes	# edges	average	maximum	minimum
0	10,601	324,167	60	703	1
1	5	14	4	5	4
2	2	3	2	2	2
3	20	51	5	17	3
4	4	10	4	4	4
5	8	35	7	8	7
6	3	6	3	3	3
7	4	4	2	2	2
8	1	1	1	1	1
9	2	2	1	2	1
10	3	6	3	3	3
11	3	2	1	2	1
12	2	3	2	2	2
13	1	1	1	1	1
total	10,659	324,305	60	703	1

Table 4. Sub-cellular localization scheme and co-localized interacting proteins in the human protein interactions derived from the yeast protein interactions.

	compartment	# interactions	# proteins
1	extracellular	18	16
2	cell wall	0	0
3	membrane	1,125	352
4	cytoplasm	1,849	432
5	cytoskeleton	1	1
6	ER	60	40
7	golgi	89	36
8	transport vesicles	0	0
9	nucleus	4,146	823
10	mitochondria	95	71
11	peroxisome	0	0
12	endosome	6	6
13	vacuole	0	0
14	microsomes	1	1
15	lipid particles	0	0
16	lysosome	3	4

Table 5. Interactions between proteins in the adjacent compartments, added to the co-localized interactions for the refinement of the initially predicted interaction data of Table 4. The membrane_cytoplasm, for example, indicates the interactions between membrane proteins and cytoplasm proteins.

	adjacent compartments	# interactions	# proteins
1	membrane_cytoplasm	1,728	644
2	golgi_cytoplasm	126	74
3	mitochondria_cytoplasm	92	61
4	nucleus_cytoplasm	5	9
5	endosome_cytoplasm	1	2
6	ER_cytoplasm	2	3

Table 6. Co-localized interacting proteins in the human protein interactions at the superfamily level. The total number of proteins involved in these interactions is 783.

sub-cellular localization	# interactions
Nucleus	4,412
Membrane	3,788
Cytoplasm	2,044
mitochondria	254
extracellular	123
Lysosome	48
endoplasmic reticulum (ER)	36
Golgi	18
Microsomes	7
Peroxisome	7
Total	10,737

Figure1. (A) The assignment of superfamilies to human proteins. (ver. 7.29) (B) The assignment of superfamilies to human proteins. (ver. 16.33.1)

Figure 2. The distribution of the node degrees of the human protein interaction network refined by the sub-cellular localization information.

Figure 3. The navy blue plot represents the distribution of the node degrees of the initial human protein interaction network, derived from the yeast protein interactions. The organce plot represents the distribution of the node degrees of the refined network by the sub-cellular localization information. The green plot represent the distribution of the node degrees in the experimental data of human protein interactions in the BIND and DIP databases.