Table 1 Protein–protein interaction sets used in the study.

Interaction set	Source of interaction data*	Number of proteins in human mapped interactions†	Number of human mapped interactions‡	References	Comments
HPRD set	Published reports	6005	19 728	5	Downloaded October 21 2005
Human Y2H set	High throughput experiments (Y2H)	2686	5211	7, 8	Interactions from both experiments pooled
Fly set	High throughput experiment (Y2H)	4706	16 313	10	All interactions were used, regardless of confidence level
Worm set	High throughput experiment (Y2H)	1933	5771	11	Downloaded from DIP database12
Yeast set	High throughput experiments (Y2H, PCP)	2455	27 098	Y2H: 13, 14 PCP: 15, 16	Interactions from all four experiments pooled
Combined high throughput set	All high throughput sets	8162	54 048	See above	Excluding HPRD
Total combined set	All interaction sets	10 894	72 940	See above	Including HPRD

*Y2H, yeast two‐hybrid protein–protein interaction assay; PCP, protein complex purification experiment (based on mass spectrometry).

†These are the proteins that could be automatically mapped to human Ensembl gene IDs.

‡These are the interactions from the original interaction sets that could be automatically mapped to human Ensembl gene IDs.