Skip to main content

Table 2 AraCyc pathways that are over-represented for comparisons 6 h vs. 0 h, 24 h vs. 0 h, and 72 h vs. 0 h based on Gene Set Enrichment Analysis

From: Phytohormone balance and stress-related cellular responses are involved in the transition from bud to shoot growth in leafy spurge

AraCyc pathways

6 h vs. 0 h

24 h vs. 0 h

72 h vs. 0 h

13-LOX and 13-HPL pathway

    

2,4,6 trinitrotoluene degradation

    

 

Abscisic acid glucose ester biosynthesis

    

Ajugose biosynthesis (galactinol-dependent)

    

Ajugose biosynthesis II (galactinol-independent)

    

Beta-alanine biosynthesis I

     

Brassionosteriod biosynthesis II

     

Calvin cycle

  

  

Cellulose biosynthesis

   

  

Chlorophyll a biosynthesis II

   

  

Chlorophyllide a biosynthesis

    

 

choline biosynthesis II

   

  

Chloline biosynthesis III

   

  

Chorismate biosynthesis

   

  

Coumarin biosynthesis (via 2-coumarate)

 

 

 

Cuticular wax biosynthesis

 

   

Cutin biosynthesis

   

 

Cyanate degradation

     

Cysteine biosynthesis

    

 

Cytokinins 7-N-glucoside biosynthesis

    

Cytokinins 9-N-glucoside biosynthesis

    

Cytokinins-O-glucoside biosynthesis

    

Ethylene biosynthesis from methionine

   

 

Fatty acid biosynthesis-initial steps

 

    

Flavonoid biosynthesis

 

 

 

Flavonol biosynthesis

   

  

Galactose degradation I

 

    

Galactose degradation II (III)

     

Galactosylcyclitol biosynthesis

    

Gluconeogenesis

 

 

Glucosinolate biosynthesis from dihomomethionine

 

    

Glucosinolate biosynthesis from hexahomome thionine

 

    

Glucosinolate biosynthesis from pentahomomethionine

 

    

Glucosinolate biosynthesis from phenylalanine

    

Glucosinolate biosynthesis from tetrahomomethionine

 

    

Glucosinolate biosynthesis from trihomomethionine

 

    

Glucosinolate biosynthesis from tryptophan

    

Glycolipid desaturation

 

    

Glycolysis I (plant cytosol)

   

  

Glycolysis II (plant plastids)

   

  

Homogalacturonan biosynthesis

   

  

Homogalacturonan degradation

  

 

Hydroxyjasmonate sulfate biosynthesis

 

    

IAA biosynthesis I

  

   

IAA biosynthesis II

     

IAA biosynthesis VII

 

    

IAA degradation IV

    

Jasmonic acid biosynthesis

  

 

Kaempferol glucoside biosynthesis (Arabidopsis)

    

Leucine degradation

  

   

Leucodelphin biosynthesis

 

  

Methionine biosynthesis

   

  

Methionine salvage pathway

   

  

Methylindole-3-acetate interconversion

 

 

 

Methylquercetin biosynthesis

   

  

Monolignol glucosides biosynthesis

    

Oxidative ethanol degradation I

  

   

Pelargonidin conjugates biosynthesis

    

Phenylalanine degradation III

  

   

Phenylpropanoid biosynthesis

 

   

Phosphatidylcholine biosynthesis IV

   

  

Phospholipases

   

 

Phospholipid desaturation

 

    

Photorespiration

 

   

Photosynthesis

 

 

Photosynthesis, light reaction

 

 

 

Plastoquinone-9 biosynthesis

   

  

Pyridine nucleotide cycling (plants)

  

   

Quercetin glucoside biosynthesis

    

Quercentinsulphates biosynthesis

   

  

Rubisco shunt

   

  

Salicylic acid biosynthesis

    

SAM cycle

   

  

S-methylmethionine cycle

   

  

Sphingolipid biosynthesis (plants)

     

Starch biosynthesis

 

 

 

Starch degradation

 

   

Suberin biosynthesis

 

   

Sucrose degradation to ethanol and lactate (anaerobic)

  

 

Superpathway of acetyl-CoA biosynthesis

   

  

Superpathway of anthocyanin biosynthesis (from cyanidin and cyanidin3-O-glucoside)

 

    

Superpathway of choline biosynthesis

   

 

Superpathway of cytosolic glycolysis (plants),pyruvate dehydrogenase and TCA cycle

  

  

Superpathway of fatty acid biosynthesis

 

    

Superpathway of lysine, threonine, and methionine biosynthesis

   

  

Superpathway of phenylalanine and tyrosine biosynthesis

 

 

  

Superpathway of phenylalanine, tyrosine and tryptophan biosynthesis

   

  

Superpathway of phosphatidylcholine biosynthesis

   

  

Superpathway of plastoquinone biosynthesis

   

  

Superpathway of starch degradation to pyruvate

   

  

Superpathway of sucrose and starch metabolism I (non-photosynthetic tissue)

 

 

Superpathway of sucrose and starch metabolism II (photosynthetic tissue)

 

    

Superpathway of sucrose degradation to pyruvate

   

 

Trehalose biosynthesis

 

 

 

Triacylglycerol biosynthesis

 

    

Triacylglycerol degradation

   

Ubiquinone-9 bipsynthesis (eukaryotic)

   

  

UDP-D-xylose biosynthesis

   

  

UDP-sugars interconversion

   

  

Very long chain fatty acid biosynthesis

 

    

Vitamin E biosynthesis

   

  

Xylan biosynthesis

    

 

Zeaxanthin biosynthesis

 

    
  1. Up and down arrows indicate the direction of regulation in the former part of the comparison (i.e., 6 h vs. 0 h: up means up in 6 h). Genes and additional data within each pathway for each comparison are available in Additional file 5: Table S4