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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