Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

Table 2 A comparison of the contributions of each dataset to the composite human protein interaction map, with network properties of each of the datasets

Dataset	Version	Number of interactions	Number of proteins	Clustering <C>	Connectivity <#interactions/protein>
Reactome	08/03/04	9,987	619	0.74	15.4
BIND	08/03/04	1,536	1,212	0.1	1.3
HPRD	04/12/04	6,054	2,747	0.09	2.2
Orthology inferred (core)	03/31/04	9,283	3,469	0.13	2.7
Co-citation	This paper	6,580	3,737	0.3	1.8
Total	This paper	31,609	7,748	0.24	4.1

An analysis of network features (clustering coefficient [38] and degree of connectivity) of each of the datasets indicates low degree (<k>) for all except Reactome, which is by far the most densely sampled protein interaction dataset. The final combined network is modular in structure and shows extensive, non-random clustering of proteins as compared to randomly generated networks with equal numbers of proteins and interactions (<C> = 9 × 10^-3 ± -3 × 10^-5; average of 10 trials).

ISSN: 1474-760X