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Table 2 A list and additional relevant information of all the gene ontology terms that present a significant enrichment in one of the six groups of genome-wide gene coordinated to one of three groups of highly coordinated genes (HCGs).

From: Coordinations between gene modules control the operation of plant amino acid metabolic networks

Coordination

Enrichment

(Log2)

# of genes in a group

# of genes in the genome

Biological process (GO)

Asp-family Met met. Group

Positive (920 genes)

3.04

4

10

syncytium formation

 

2.88

5

14

protein targeting to mitochondrion

 

2.86

6

17

microtubule-based process

 

2.77

31

94

ribosome biogenesis and assembly

 

2.69

5

16

cellular protein metabolic process

 

2.67

4

13

nucleocytoplasmic transport

 

2.56

12

42

chromosome organization and biogenesis

 

2.47

91

340

translation

 

2.44

5

19

response to UV

 

2.42

7

27

translational elongation

 

2.31

13

54

nucleosome assembly

 

2.23

5

22

sterol biosynthetic process

 

1.73

9

56

fatty acid biosynthetic process

 

1.44

17

129

transmembrane receptor protein tyrosine kinase signaling pathway

 

-1.62

12

762

regulation of transcription, DNA-dependent

Negative (1780 genes)

2.76

7

11

heat acclimation

 

2.66

16

27

response to hydrogen peroxide

 

2.57

5

9

response to water

 

2.51

15

28

response to high light intensity

 

2.41

9

18

cold acclimation

 

2.26

9

20

trehalose biosynthetic process

 

2.24

8

18

response to desiccation

 

2.05

19

49

response to osmotic stress

 

2.03

33

86

response to heat

 

1.98

36

97

response to water deprivation

 

1.9

55

157

response to abscisic acid stimulus

 

1.89

8

23

fatty acid beta-oxidation

 

1.87

25

73

response to wounding

 

1.86

16

47

response to cadmium ion

 

1.79

11

34

abscisic acid mediated signaling

 

1.76

14

44

toxin catabolic process

 

1.68

47

156

response to salt stress

 

1.57

25

90

response to ethylene stimulus

 

1.47

36

139

response to cold

 

1.34

19

80

response to stress

 

1.29

23

100

response to jasmonic acid stimulus

 

1.26

20

89

response to salicylic acid stimulus

Asp-family Catabolic group

Positive (536 genes)

3.21

6

23

fatty acid beta-oxidation

 

2.75

4

21

tryptophan biosynthetic process

 

2.71

5

27

response to hydrogen peroxide

 

2.66

13

73

response to wounding

 

2.27

6

44

toxin catabolic process

 

2.27

6

44

aging

 

2.15

6

48

defense response to fungus

 

2.13

12

97

response to water deprivation

 

2.1

19

157

response to abscisic acid stimulus

 

1.92

13

122

multicellular organismal development

 

1.89

9

86

response to heat

 

1.77

15

156

response to salt stress

 

1.62

13

150

response to oxidative stress

 

1.61

12

139

response to cold

Negative (2451 genes)

2.69

5

6

purine nucleotide biosynthetic process

 

2.54

6

8

pentose-phosphate shunt, non-oxidative branch

 

2.44

66

94

ribosome biogenesis and assembly

 

2.18

199

340

translation

 

2.04

9

17

microtubule-based process

 

2.01

14

27

translational elongation

 

1.95

8

16

cellular protein metabolic process

 

1.95

21

42

chromosome organization and biogenesis

 

1.89

11

23

tRNA aminoacylation for protein translation

 

1.83

11

24

chlorophyll biosynthetic process

 

1.72

23

54

nucleosome assembly

 

1.32

18

56

fatty acid biosynthetic process

 

1.11

36

129

transmembrane receptor protein tyrosine kinase signaling pathway

 

1.02

52

199

protein folding

 

-0.74

66

851

protein amino acid phosphorylation

 

-0.93

36

530

regulation of transcription

 

-1.08

22

359

N-terminal protein myristoylation

 

-1.19

43

762

regulation of transcription, DNA-dependent

 

-1.82

12

329

defense response

 

-2.37

5

200

ubiquitin-dependent protein catabolic process

Aromatic amino acids (AAA) group

Positive (498 genes)

4.96

4

5

negative regulation of programmed cell death

 

4.14

5

11

phenylpropanoid biosynthetic process

 

4.11

4

9

phenylpropanoid metabolic process

 

3.47

4

14

aromatic amino acid family biosynthetic process

 

3.35

5

19

response to fungus

 

3.21

5

21

tryptophan biosynthetic process

 

3.14

5

22

cell wall catabolic process

 

3

15

73

response to wounding

 

2.86

9

48

defense response to fungus

 

2.65

5

31

lignin biosynthetic process

 

2.37

6

45

defense response to bacterium

 

2.14

5

44

toxin catabolic process

 

1.86

14

150

response to oxidative stress

 

1.74

12

139

response to cold

 

1.3

54

851

protein amino acid phosphorylation

Negative (2466 genes)

2.94

6

6

glycine decarboxylation via glycine cleavage system

 

2.94

5

5

protein import into chloroplast thylakoid membrane

 

2.94

4

4

water transport

 

2.94

4

4

photosynthesis, light harvesting

 

2.94

4

4

cellulose and pectin-containing primary cell wall biogenesis

 

2.94

4

4

amylopectin biosynthetic process

 

2.75

7

8

photosystem II assembly

 

2.68

5

6

protein import into chloroplast stroma

 

2.68

5

6

isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway

 

2.68

5

6

carotene biosynthetic process

 

2.65

9

11

starch catabolic process

 

2.53

6

8

thylakoid membrane organization and biogenesis

 

2.48

8

11

reductive pentose-phosphate cycle

 

2.36

16

24

chlorophyll biosynthetic process

 

1.88

11

23

ATP-dependent proteolysis

 

1.77

12

27

chloroplast organization and biogenesis

 

1.51

20

54

photosynthesis

 

1.31

18

56

fatty acid biosynthetic process

 

-0.62

72

851

protein amino acid phosphorylation

 

-0.99

50

762

regulation of transcription, DNA-dependent

 

-1.22

20

359

N-terminal protein myristoylation

 

-1.72

13

329

defense response