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Table 1 Consistency of the twenty-nine networks with expression profiles measured under anaerobic conditions in Escherichia coli

From: Network evaluation from the consistency of the graph structure with the measured data

No.

ID

Description

node

edge

GCP

1

C9333

detoxification

6

8

1.000

2

C9448

amino acids

6

9

1.000

3

C9449

carbon compounds

6

9

1.000

4

C9426

colanic acid (M antigen)

6(7)

9(11)

1.000

5

C9509

operon

6(7)

9(11)

1.000

6

C9448, C9462

amino acids, formyl-THF biosynthesi

7

10

1.000

7

C9449

carbon compounds

8(9)

7(8)

1.000

8

C9331

motility, chemotaxis, energytaxis

9

8

0.998

9

C9340

flagella

9

8

0.647

10

C9362

nucleoproteins, basic proteins

9

8

0.925

11

C9401

tryptophan

9

8

1.000

12

C9449

carbon compounds

9

8

1.000

13

C9376

cytoplasm

10

9

1.000

14

C9449

carbon compounds

10

9

0.006

15

C9449

carbon compounds

10

11

0.976

16

C9337

SOS response

11

10

0.127

17

C9354

DNA repair

11

10

0.068

18

C9383

arginine

11

10

1.000

19

C9474

nucleotide and nucleoside conversion

11

15

0.378

20

C9493

fermentation

11

10

1.000

21

C9376

cytoplasm

12

11

0.302

22

C9393

isoleucine/valine

13

12

1.000

23

C9420

purine biosynthesis

13

12

1.000

24

C9394

leucine

14

17

1.000

25

C9504

phosphorous metabolism

23

22

1.000

26

C9528

repressor

52(53)

77(79)

1.000

27

C9523

activator

58(59)

92(93)

1.000

28

C9490

anaerobic respiration

89(91)

161(162)

0.016

29

C9372

Transcription related

91(93)

143(146)

0.772

  1. GCP values with less than 5% significance probability are indicated in bold type. The ID in the classification scheme by EcoCyc [44] and the corresponding gene function are denoted in the second and third columns, respectively. Two networks in the functions C9448 and C9462 are composed of the same constituent genes with the same connectivity. In the following columns, the numbers of nodes and edges of the analyzed networks are denoted: the original network was constructed based on the information about the relationship between the transcription factor and its regulated genes in EcoCyc, and the analyzed network was constructed from the original network by excluding the genes that were not found in the expression profile data from NCBI GEO (accession number: GSE1107) [25]. The numbers of nodes and edges of the original networks are denoted in parentheses. The graph consistency probability (GCP) is denoted in the last column.