Table 2 Dysregulated pathways with significantly changed expression correlations.

From: Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

Pathway IDa

Pathway Name

#Gene

#DEGb

P_scorec

P-valued

SUCSYN-PWY*

Sucrose biosynthesis I

45

20

1.79

<1.00 × 10−03

PWY-5046

2-Oxoisovalerate decarboxylation to isobutanoyl-CoA

10

2

2.34

<1.00 × 10−03

CITRULBIO-PWY

Citrulline biosynthesis

26

7

2.02

<1.00 × 10−03

PWY-101*

Photosynthesis light reactions

35

30

2.60

<1.00 × 10−03

THRESYN-PWY

Threonine biosynthesis

19

4

2.00

<1.00 × 10−03

PWY66-21

Ethanol degradation II

22

9

1.95

<1.00 × 10−03

GLYCLEAV-PWY*

Glycine cleavage

10

5

2.36

<1.00 × 10−03

PWY-7328

Super pathway of UDP-glucose-derived O-antigen building blocks biosynthesis

28

5

1.99

<1.00 × 10−03

PWY-5464*

Super pathway of cytosolic glycolysis, pyruvate dehydrogenase and TCA cycle

110

31

1.56

<1.00 × 10−03

PWY-622*

Starch biosynthesis

27

12

1.90

<1.00 × 10−03

CALVIN-PWY*

Calvin-Benson-Bassham cycle

37

25

1.87

<1.00 × 10−03

COLANSYN-PWY

Colanic acid building blocks biosynthesis

38

7

1.93

<1.00 × 10−03

PHOTOALL-PWY*

Oxygenic photosynthesis

72

55

2.14

<1.00 × 10−03

PWY-5004

Super pathway of citrulline metabolism

31

7

1.98

<1.00 × 10−03

PWYQT-4470

γ-Glutamyl cycle

3

0

4.84

<1.00 × 10−03

NONOXIPENT-PWY

Pentose phosphate pathway

12

6

2.43

<1.00 × 10−03

GLUTATHIONESYN-PWY

Glutathione biosynthesis

2

0

8.30

<1.00 × 10−03

PWY-5723*

Rubisco shunt

35

17

1.80

<1.00 × 10−03

CAROTENOID-PWY*

Super pathway of carotenoid biosynthesis

20

11

2.03

2.04 × 10−02

PWY-5805

Nonaprenyl diphosphate biosynthesis I

2

2

6.63

2.04 × 10−02

PWY-4302

Aerobic respiration III

56

4

1.63

2.04 × 10−02

PWY-6415

L-ascorbate biosynthesis V

23

5

1.99

2.04 × 10−02

PWY-2501

Fatty acid α-oxidation I

10

6

2.45

2.04 × 10−02

HOMOSERSYN-PWY

Homoserine biosynthesis

7

1

2.72

2.04 × 10−02

TYRFUMCAT-PWY*

Tyrosine degradation I

8

2

2.66

2.04 × 10−02

HEXPPSYN-PWY

Hexaprenyl diphosphate biosynthesis

2

2

6.63

2.04 × 10−02

COMPLETE-ARO-ARA-PWY*

Super pathway of phenylalanine, tyrosine and tryptophan biosynthesis

26

10

1.94

2.04 × 10−02

PWY-5114*

UDP-sugars interconversion

29

5

1.78

3.24 × 10−02

PWY-1422

Vitamin E biosynthesis

6

3

2.72

3.24 × 10−02

PWY-6444

Benzoate biosynthesis II

12

7

2.10

3.24 × 10−02

PWY-601*

Glucosinolate biosynthesis from tryptophan

25

7

1.78

3.24 × 10−02

PWYQT-4450*

Aliphatic glucosinolate biosynthesis, side chain elongation cycle

7

4

2.53

3.24 × 10−02

PWY-5783

Octaprenyl diphosphate biosynthesis

2

2

6.63

3.24 × 10−02

GLUTAMINDEG-PWY

Glutamine degradation I

18

5

1.99

3.24 × 10−02

TRPSYN-PWY*

Tryptophan biosynthesis

14

7

2.06

4.59 × 10−02

PWY-181*

Photorespiration

26

12

1.72

4.59 × 10−02

  1. aThe pathways detected as significant through the GSEA analysis are marked with asterisk.
  2. bDEGs were detected using the R package maSigPro.
  3. cP_scores are calculated using Eq. 4.
  4. dp-values were corrected using the Benjamini-Hochberg correction.
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