Table 2

Comparison of novel interactions identified by ChIP-chip experiments, CLR, SEREND and DISTILLER for five global regulators

Predictions

Not ChIP-chip

ChIP-chip

Total

Recall

Precision

FNR

ChIP-chip

-

73

73

CLR

14

0

14

0

0

SEREND

76

19

95

0.26

0.20

DISTILLER

21

4

25

0.055

0.16

CRP

ChIP-chip

-

57

57

CLR

23

0

23

0

0

SEREND

203

9

212

0.16

0.042

DISTILLER

57

6

63

0.11

0.095

Fis

ChIP-chip

-

179

179

CLR

59

4

63

0.022

0.06

SEREND

33

4

37

0.022

0.11

DISTILLER

17

3

20

0.017

0.15

H-NS

ChIP-chip

-

82

82

CLR

26

0

26

0

0

SEREND

4

0

4

0

0

DISTILLER

0

0

0

0

0

IHF

ChIP-chip

-

110

110

CLR

67

4

71

0.036

0.056

SEREND

79

10

89

0.091

0.11

DISTILLER

14

4

18

0.036

0.22

For each method, the identified interactions that were novel as compared to RegulonDB were selected. For all novel interactions, we indicate whether (ChIP-chip) or not (Not ChIP-chip) the interactions were found in a corresponding ChIP-chip experiment. The recall (TP/TP + FN) and precision (TP/TP + FP) were calculated using the ChIP-chip data as a gold standard. Interactions identified by either CLR, SEREND or DISTILLER and confirmed by a ChIP-chip experiment were considered to be true positives (TP); interactions confirmed by a ChIP-chip experiment but not identified by either CLR, SEREND or DISTILLER were considered false negatives (FN); interactions identified by either CLR, SEREND or DISTILLER but not confirmed in a ChIP-chip experiment were considered false positives (FP).

Lemmens et al. Genome Biology 2009 10:R27   doi:10.1186/gb-2009-10-3-r27