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Table 2 Co-occurrence Correspondence to Annotation

From: Improving protein function prediction methods with integrated literature data

Mutual Information Measure (MUT)

Fraction

Yeast

MIPS

MF

BP

Worm

MF

BP

Fly

MF

BP

> 0.0

8621

80

41

71

21847

76

57

17508

47

70

≥0.1

8615

80

41

71

21711

77

57

17422

47

70

≥0.2

8554

80

41

71

21177

78

58

16753

47

71

≥0.3

8210

80

41

71

20209

80

60

14494

49

72

≥0.4

7216

80

43

72

18811

83

63

10625

53

76

≥0.5

5592

82

46

73

17813

85

64

7021

56

76

≥0.6

3605

82

51

74

15857

91

67

4112

63

74

≥0.7

1856

82

56

74

12770

91

61

1965

59

68

≥0.8

700

77

54

72

10924

94

61

1002

56

63

≥0.9

159

65

45

75

6360

94

91

308

38

40

Hypergeometric Measure (HYG)

Fraction

Yeast

MIPS

MF

BP

Worm

MF

BP

Fly

MF

BP

>0.0

8621

80

43

73

21847

76

57

17508

47

70

≥0.1

8614

80

43

73

21739

77

57

17125

47

71

≥0.2

8607

80

43

73

21680

77

57

17044

47

71

≥0.3

8600

80

43

73

21671

77

57

16907

47

71

≥0.4

8591

80

43

73

21397

78

58

16719

47

71

≥0.5

8572

80

43

73

21202

78

58

16575

48

71

≥0.6

8557

80

43

73

21183

78

58

16360

48

71

≥0.7

8532

80

44

73

21159

78

58

16060

48

71

≥0.8

8466

80

44

73

20650

79

59

15665

48

71

≥0.9

8368

80

44

73

20386

80

60

14764

49

72

Asymmetric Co-occurrence Fraction Measure (ACF)

Fraction

Yeast

MIPS

MF

BP

Worm

MF

BP

Fly

MF

BP

>0.0

8621

80

41

71

21847

76

57

17508

47

70

≥0.1

6220

82

45

73

20063

80

60

9610

56

75

≥0.2

4241

82

49

74

17836

84

63

6786

58

76

≥0.3

2947

82

54

76

17353

86

63

5078

61

76

≥0.4

2283

82

56

76

17023

87

64

4178

64

77

≥0.5

1745

80

55

74

16875

87

63

3589

66

77

≥0.6

1195

78

55

73

16574

88

64

2922

68

76

≥0.7

713

78

56

72

16082

88

64

2494

70

76

≥0.8

536

74

52

69

15938

89

63

2277

71

77

≥0.9

390

68

47

65

15821

89

64

2031

72

75

  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 in the columns labeled by organism name. Abbreviations: GO SLIM Molecular Function (MF), GO SLIM Biological Process (BP).