A human functional protein interaction network and its application to cancer data analysis

Table 1 Data sources used to predict protein functional interactions

Data source	Proteins	SwissProt proteins (coverage)	Interactions	Reference
Human PPIs	10,287	10,029 (49%)	53,743	[45–47]
Fly PPIs	13,383	4,088 (20%)	939,639 (26,346^a)	[45]
Worm PPIs	5,223	1,477 (7%)	122,192 (8,161^a)	[45]
Yeast PPIs	5,646	1,530 (8%)	1,900,980 (167,574^a)	[45]
Domain interaction	60,569	15,218 (75%)	NA	[52]
Lee's Gene Expression	8,250	7,647 (38%)	206,117	[49]
Prieto's Gene Expression	3,024	2,901 (14%)	13,441	[50]
GO BP sharing	14,197	14,197 (70%)	NA	[51]
PPIs from GeneWays	5,252	5,252(26%)	51,048	[53]

To calculate the coverage of SwissProt, we used 20,332, the total identifier number in SwissProt (UniProtKB/Swiss-Prot Release 56.9, 3 March 2009), as the denominator. The numbers of interactions from three model organisms have been mapped to human proteins based on Ensembl Compara [48] (see text for details). ^aNumbers of PPIs in the original species. BP, biological process.

ISSN: 1474-760X