Table 1

Comparison of different heuristics.

BowTieBuilder

shortest paths

all shortest paths

all interactions

G1-Phase

precision (PPI)

77%

77%

77%

48%

recall (PPI)

77%

77%

77%

77%

precision (protein)

67%

67%

67%

67%

recall (protein)

67%

67%

67%

67%

S-Phase

precision (PPI)

73%

70%

59%

60%

recall (PPI)

55%

60%

50%

56%

precision (protein)

86%

86%

86%

86%

recall (protein)

86%

86%

86%

86%

MAPK

precision (PPI)

46%

46%

37%

31%

recall (PPI)

37%

43%

45%

41%

precision (protein)

79%

80%

69%

79%

recall (protein)

74%

78%

80%

74%

Erb

precision (PPI)

55%

40%

9%

NA

recall (PPI)

28%

25%

15%

NA

precision (protein)

79%

72%

44%

79%

recall (protein)

56%

76%

73%

56%

average

precision (PPI)

63%

58%

46%

46%

recall (PPI)

49%

51%

47%

58%

precision (protein)

78%

76%

67%

78%

recall (protein)

71%

77%

77%

71%

Statistical evaluation of signal transduction pathways inferred with BowTieBuilder and alternative heuristics. The inferred signal transduction pathways are mapped against the reference signal transduction pathways from KEGG. The precision and recall rates are calculated with respect to the PPIs and proteins.

Supper et al. BMC Systems Biology 2009 3:67   doi:10.1186/1752-0509-3-67