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Table 1 Physical and Genetic Correspondence to Annotation

From: Improving protein function prediction methods with integrated literature data

PHYSICAL

Yeast

MIPS

MF

BP

Worm

MF

BP

Fly

MF

BP

Uetz 1498

37

15

32

Y2H 2619

10

6

Y2H 20045

10

14

Ito 4469

19

8

17

Aff Chr 26

19

0

Immunoblotting 2

100

100

Fromont 175

26

15

37

   

Immuno Prec 5

60

100

Gavin 3139

67

41

70

   

Gel Retardation 2

100

100

Ho 3464

38

15

36

   

Experimental 1

100

100

       

Biophysical 3

100

100

       

Alanine Scanning 2

100

100

GENETIC

Yeast

MIPS

MF

BP

Worm

MF

BP

Fly

MF

BP

Bellaoui 34

79

0

82

All 20543

42

50

All 6523

32

69

Davierwala 564

40

13

39

      

Huang 58

55

5

55

      

Goehring 63

65

5

61

      

Kozminski 30

70

7

53

      

Krogan 36

50

11

78

      

Parsons 86

55

2

43

      

Tong 5907

49

12

39

      
  1. Percentage of edges in the full graph which connect proteins sharing the same annotation according to the gold standard. These values are the r i used in the calculation of edge weights by the noisy-or function. The number of edges scored is shown following the experimental group name. Listed by first author, PubMed identifiers for the groups are: Uetz PMID:10688190, Ito PMID:10655498, PMID:11283351, Fromont PMID:9207794, Gavin PMID:11805826, Ho PMID:11805837, Bellaoui PMID:12912927, Davierwala PMID:16155567, Huang PMID:12077337, Goehring PMID:12686605, Kozminski PMID:12960420, Krogan PMID:12773564, Parsons PMID:14661025, and Tong PMID:14764870. Abbreviations: GO SLIM Molecular Function (MF), GO SLIM Biological Process (BP), yeast two-hybrid (Y2H), affinity chromatography (Aff Chr), immunoprecipitation (Immuno Prec).
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BMC Bioinformatics

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