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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





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






Phospholipid desaturation









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