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Table 1 Data sources used to predict protein functional interactions

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

Data source

Proteins

SwissProt proteins (coverage)

Interactions

Reference

Human PPIs

10,287

10,029 (49%)

53,743

[4547]

Fly PPIs

13,383

4,088 (20%)

939,639 (26,346a)

[45]

Worm PPIs

5,223

1,477 (7%)

122,192 (8,161a)

[45]

Yeast PPIs

5,646

1,530 (8%)

1,900,980 (167,574a)

[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]

  1. 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.