Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli




Table 2. Position of three-node subgraphs (CON, DIV, CAS, FFL) within the E. coli transcriptional regulatory network

CON (227)

Type

Total

Dist = 0

Dist = 1

Dist = 2

Dist = 3

Dist = 4

Input

X

62

47

13

1

1

0

Y

86

0

48

35

1

2

X,Y

146

47

60

35

2

2

Output

X

62

0

44

12

5

1

Y

86

79

5

2

0

0

X,Y

146

79

48

13

5

1

DIV (4777)

Type

Total

Dist = 0

Dist = 1

Dist = 2

Dist = 3

Dist = 4

Input

X

59

39

16

3

1

0

Y

316

0

211

85

8

12

X,Y

356

39

212

85

8

12

Output

X

59

0

37

15

5

2

Y

316

287

23

4

2

0

X,Y

356

287

47

15

5

2

CAS (160)

Type

Total

Dist = 0

Dist = 1

Dist = 2

Dist = 3

Dist = 4

Input

X

23

17

5

1

0

0
 

Y

25

0

18

6

1

0

Z

87

0

0

65

10

12

X,Y,Z

122

17

18

65

10

12

Output

X

23

0

0

16

5

2

Y

25

0

19

4

2

0

Z

87

79

7

1

0

0

X,Y,Z

122

79

20

16

5

2

FFL (42)

Type

Total

Dist = 0

Dist = 1

Dist = 2

Dist = 3

Dist = 4

Input

X

10

6

3

1

0

0

Y

19

0

14

4

1

0

Z

42

0

0

32

5

5

X,Y,Z

67

6

15

36

5

5

Output

X

10

0

0

4

5

1

Y

19

0

14

4

1

0

Z

42

40

2

0

0

0

X,Y,Z

67

40

15

6

5

1

The number of X-, Y-, Z-type nodes located at distances of 0, 1, 2, 3 and 4 links (columns) from the input layer (first rows for each subgraph) and from the output layer (last rows for each subgraph) is listed.

This Article

  1. Published online before print May 20, 2005, doi: 10.1073/pnas.0500365102 PNAS May 31, 2005 vol. 102 no. 22 7841-7846
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