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Table 1 Biological validation of LeMoNe on E. coli

From: Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Regulator

Module ID

Score

Target enrich.

Autoreg.

Pathway

Local

Function

gatR_2

73

1912.98

**

 

*

**

carbon utilization > carbon compounds

gadE

48

1844.50

**

*

*

**

adaptations > pH

gutM

38

1807.24

**

*

*

*

carbon utilization > carbon compounds

ymfN

58

1749.11

   

*

 

ymfN

33

1711.17

   

*

 

fliA

12

1510.48

**

*

*

**

motility, chemotaxis, energytaxis; flagella; biosynthesis of flagellum

rcsB

62

1261.72

  

*

*

biosynthesis of colanic acid (M antigen)

fecI

57

1200.77

 

*

*

 

adaptations > Fe aquisition

gatR_2

42

1176.55

**

 

*

**

carbon utilization > carbon compounds

yahA

82

1171.92

     

rcsA

87

1151.97

**

*

*

 

biosynthesis of colanic acid (M antigen)

lexA

20

996.62

**

*

*

*

SOS response; DNA repair; protection > radiation

lldR

65

976.84

**

*

*

*

energy metabolism; aerobic respiration

fliA

45

956.70

**

*

*

 

motility, chemotaxis, energytaxis

fliA

18

903.46

*

*

*

 

biosynthesis of flagellum; motility, chemotaxis, energytaxis; flagella

nac

85

827.17

 

*

*

 

nitrogen metabolism

yiaG

15

816.55

     

ydaK

23

815.75

   

**

 

ydaK

154

805.22

     

fnr

23

798.27

*

*

*

**

energy metabolism; anaerobic respiration; membrane

lrp

5

777.80

 

*

*

 

biosynthesis of building blocks > amino acids

araC

46

760.44

**

*

*

**

carbon utilization > carbon compounds

appY

50

748.75

     

yfiE

67

736.50

     

osmE

15

734.87

     

lexA

78

726.67

**

*

*

 

SOS response

purR

144

708.63

 

*

*

  

uidR

81

708.36

 

*

   

araC

21

678.10

*

*

*

 

carbon utilization > carbon compounds

yfeG

29

663.94

     

b1450

53

662.16

     

flhC

18

650.64

**

 

*

 

biosynthesis of flagellum; motility, chemotaxis, energytaxis; flagella

ogrK

83

645.35

     

fliA

17

637.28

 

*

   

rpoS

14

637.13

**

 

*

*

adaptations > osmotic pressure

pdhR

55

633.52

 

*

*

 

energy metabolism; anaerobic respiration

tdcA

31

619.06

*

*

*

*

threonine catabolism; carbon utilization > amino acids

yebK

106

617.44

     

araC

56

608.17

**

*

*

 

carbon utilization > carbon compounds

csgD

26

599.30

 

*

   

hycA

66

596.27

     

tdcR

11

593.75

  

*

 

carbon utilization > amino acids

fliA

24

593.05

*

*

*

 

flagella; motility, chemotaxis, energytaxis; biosynthesis of flagellum

chbR

24

590.31

 

*

   

hycA

29

563.45

   

*

 

galS

76

561.25

**

*

*

**

carbon utilization > carbon compounds

nlp

77

559.41

     

yfeC

119

549.33

     

b1506

36

548.33

     

lrp

10

528.90

*

*

*

 

biosynthesis of building blocks > amino acids

cspB

37

527.86

     

cusR

68

515.56

**

*

*

**

extrachromosomal > transposon related

b1284

51

514.78

     

nanR

9

508.87

     

yohL

90

496.21

     

lrp

126

493.60

 

*

*

 

biosynthesis of building blocks > amino acids

yjjQ

179

491.02

     

yehV

63

483.29

     

ogrK

27

481.75

     

slyA

3

474.43

     

ydcN

16

467.66

     

cpxR

9

465.39

*

*

*

 

adaptations > other (mechanical, nutritional, oxidative stress)

yehV

34

451.77

     

fruR

63

449.25

     

araC

64

441.57

*

*

*

 

carbon utilization > carbon compounds

fis

19

436.12

**

*

*

*

information transfer > RNA related > tRNA

fadR

16

435.98

*

    

purR

10

431.78

**

*

*

 

biosynthesis of building blocks > nucleotides

cadC

37

429.32

 

*

   

fecI

54

429.28

 

*

   

rstA

102

428.94

     

tdcR

61

428.84

     

flhC

24

426.88

**

 

*

*

flagella; motility, chemotaxis, energytaxis; biosynthesis of flagellum

  1. Biological validation of the LeMoNe 30% precision network for E. coli. Target enrichment: (*) module is enriched in known targets of the predicted regulator, (**) module is most enriched for predicted regulator. Autoregulator: (*) regulator is an autoregulator. Pathway: (*) module is enriched in the same function(s) as the regulator. Local: (*) regulator is in the same operon as the module genes, (**) Transcription unit of regulator is adjacent to transcription units of the module genes. Function: enriched functions of the module. Regulators in bold face are putative regulators without known targets; module IDs in bold face consist only of uncharacterized genes.
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BMC Systems Biology

ISSN: 1752-0509

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