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

Chao, Wun S.; Doğramaci, Münevver; Horvath, David P.; Anderson, James V.; Foley, Michael E.

doi:10.1186/s12870-016-0735-2

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		↓

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

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ISSN: 1471-2229

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