Table 4

New human proteins found by our method as potential interaction partners with HCV proteins

HCV protein

Known HHCV

Initial candidates of HHCV by BLAST search

Predicted candidates of HHCV by SVM

Refined candidates of HHCV with GO


core

118

732

225

71

E1

16

150

28

9

E2

29

182

33

10

F

10

206

57

12

NS2

11

176

42

8

NS3

298

1,599

495

195

NS4A

7

114

33

10

NS4B

1

1

1

1

NS5A

152

499

123

72

NS5B

36

384

92

51

p7

17

166

51

17


Total

695

4,209

1,180

456


The 'Initial candidates of HHCV by BLAST search' indicate the initial candidates of human proteins interacting with HCV proteins (called HHCV in this paper) found by BLAST search from GenBank with the known HHCV as query sequences. The 'Predicted candidates of HHCV by SVM' were determined by the SVM model from the initial candidates of HHCV. The 'Refined candidates of HHCV with GO' were obtained from the predicted candidates by selecting HHCV that have the same GO cellular component terms as the known HHCV.

Cui et al. BMC Bioinformatics 2012 13(Suppl 7):S5   doi:10.1186/1471-2105-13-S7-S5

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