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Table 2 Contributions of genomic data sources

From: Integrative approaches to the prediction of protein functions based on the feature selection

Data source

Exhaustive search

KL1LR

  

# of GO terms (# in union)

AUC

# of GO terms (# in union)

AUC

NCG

Protein-protein interactions

OPHID

192

 

0.82

201

 

0.89

83

Protein domain

Interpro

522

(697)

0.87

408

(518)

0.89

266

 

Pfam

600

 

0.86

311

 

0.89

210

Phenotype

MGI

213

 

0.87

346

 

0.90

129

Phylogenetic profile

BioMart

33

(95)

0.83

59

(166)

0.88

4

 

Inparanoid

70

 

0.84

124

 

0.88

22

Disease

OMIM

41

 

0.85

32

 

0.88

3

Gene expression

Zhang et al.

28

 

0.81

147

 

0.90

10

 

Su et al.

21

(55)

0.82

158

(309)

0.89

8

 

Sage et al.

16

 

0.83

113

 

0.90

7

  1. The numbers of GO terms satisfying the cut-off of prediction accuracies by the AUC and P20R values are presented for each data source along with the average AUC values of the GO terms. For the protein domain, phylogenetic profile, and gene expression data, the number of terms in the union set is shown in parentheses. The numbers of common terms between the two approaches are shown in the last column (NCG).