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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     
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