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Table 2 Comparison of GO mapping classification to Valle's categories

From: Evaluation of high-throughput functional categorization of human disease genes

Valle's Category

Original curation HDG count

True Positives

False Negatives

False Positives

GO-Mapping precision

GO-Mapping recall

Cell Signalling

20

11

9

20

35%

55%

Channel

32

25

7

15

61%

78%

Enzyme

232

208

24

107

66%

90%

Extracellular matrix component

54

41

13

25

62%

76%

Hormone

14

14

0

1

93%

100%

Immunoglobulin

4

1

3

2

33%

25%

Intracellular matrix component

50

23

27

207

10%

46%

Modulator of protein function

105

4

101

5

44%

4%

Receptor

86

82

4

96

46%

95%

Transcription factor

79

62

17

10

85%

78%

Transmembrane Transporter

35

42

3

102

29%

93%

Totals & overall accuracy scores

711

513

208

590*

47%**

71%**

  1. * Due to the possible assignment of more than one GO term per gene, we overestimated the overall FP rate as one gene classified multiple times due to multiple GO annotations lead to counting as a FP the same gene more than once.
  2. ** Overall accuracy scores are calculated from the overall True positive, false positive and false negative scores (they are not an average of the categorical accuracy scores)