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Table 2 Statistically significant or enriched biological processes protecting the Arabidopsis thaliana plant

From: A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1

GO ID

Process name

L

p-value

ap-value

Process functions

Stressor

Tps

RF

GO:0010200

Response to chitin

5

1.40e−11

1.04e−09

Defence against chitin bearing pathogens such as fungi, exoskeletons of animals and nematodes.

Biotic

Biotrophics

✓

GO:0000165

MAPK cascade

9

7.69e−12

5.69e−10

The process involves programmed cell death as a way of responding to biotic and abiotic factors.

Biotic

Biotrophics

✓

GO:0006612

Protein targeting to membrane

8

0.0

0.0

Directs the proteins to the cell membrane for further transportation and communication of chemicals.

Biotic & abiotic

-

✗

GO:0001666

Response to hypoxia

5

8.12e−09

6.01e−07

The response is triggered when the oxygen goes below, 20.8−20.95%.

Abiotic

-

✗

GO:0009611

Response to wounding

3

8.61e−06

6.37e−04

A biological mechanism that takes place indicating the damage of an organism.

Biotic & abiotic

Biotrophics

✓

GO:0009738

Abscisic acid (ABA)-activated signalling pathway

7

0.0

0.0

Controls environmental stress for example, drought and plant pathogens [115].

Abiotic & biotic

Necrotrophics

✓

GO:0009409

Response to cold

4

0.0

0.0

Reacts to changes in low temperatures.

Abiotic

-

✗

GO:0061025

Membrane fusion

4

0.0

0.0

Ensures life continuity in organisms.

Biotic & abiotic

Necrotrophic & biotrophics

✓

GO:0009626

Plant-type hyper-sensitive response

6

5.29e−12

3.91e−10

Killing of cells surrounding the infected area (programmed cell death) to starve pathogens like biotrophics

Biotic

Biotrophics

✓

GO:0010310

Regulation of hydrogen peroxide metabolic process

6

3.51e−11

2.60e−09

Controls plant stress and programmed cell death. It is also a go-between the wounding responses and biotic interactions.

Biotic & abiotic

Necrotrophics

✓

GO:0009697

Salicylic Acid biosynthetic process

9

2.72e−11

2.01e−09

Forms salicylic acid which is a fungicide present in some plants.

Biotic

Biotrophics

✓

GO:0002679

Respiratory burst involved in defense response

4

2.86e−11

2.12e−09

Ensures life continuity in plants when the defence response consumption rate increases for instance, the presence of phagocytic leukocytes.

Biotic

Necrotrophics & biotrophics

✓

GO:0035304

Regulation of protein dephosphorylation

8

0.0

0.0

Controls the removal rate of phosphorous, suppresses pathogenesis related expression and promotes programmed cell death.

Biotic

Biotrophics

✓

GO:0031348

Negative regulation of defence response

6

0.0

0.0

Controls the frequency of the defence response.

Biotic

Necrotrophics

✓

GO:0010363

Regulation of plant-type hyper-sensitive response

7

1.01e−11

7.51e−10

Balances the hyper-sensitive response.

Biotic

Biotrophs

✓

GO:0009862

Systemic acquired resistance, salicylic acid mediated signalling pathway

8

4.99e−12

3.70e−10

Salicylic acid plays a vital role in the expression of pathogenesis related proteins.

Biotic

Biotrophics

✓

GO:0043069

Negative regulation of programmed cell death

6

0.0

0.0

Stops the occurrence of programmed cell death.

Biotic

Necrotrophics

✓

GO:0050832

Defence response to fungus

6

2.41e−11

1.78e−09

Protects the cell plants from fungi.

Biotic

Necrotrophics & biotrophics

✓

GO:0009410

Response to xenobiotic stimulus

3

4.06e−06

3.00e−04

Takes place when the system identifies foreign compounds in the organism.

Biotic

Necrotrophics & biotrophics

✓

GO:0010112

Regulation of systemic acquired resistance

7

1.70e−04

0.0126

Balancing of systemic acquired resistance.

Biotic

Biotrophics

✓

GO:0016045

Detection of bacterium

6

4.11e−11

3.04e−09

Converts the signal of presence of bacteria into a molecular signal.

Biotic

Necrotrophics & biotrophic

✓

  1. For each process identified, following information is provided: Level (L) in the GO directed acyclic graph structure, p-value and adjusted p-value (ap-value), functional activities triggered, nature of stress thwarted, type of pathogens suppressed (Tps) and whether it contributes to response to fungi (RF) or not