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Table 2 Overrepresented GO terms in leaves and roots DEGs

From: Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves

Leaves description: biological processes GO terms DEGs P-value
DNA unwinding involved in replication GO:0006268 7 0
Membrane disassembly GO:0030397 12 0
Wax biosynthesis and metabolism GO:0010025, GO:0010166 12 0
Defense response to bacterium GO:0009816 14 0
DNA methylation GO:0006306 11 0
Lipid metabolism GO:0006629 76 0
Single-organism biosynthesis and metabolism GO:0044710, GO:0044711 167 0
Organic hydroxy compound biosynthesis and metabolism GO:0006066, GO:1901615, GO:1901617 30 0.005
Negative regulation of developmental growth GO:0048640 3 0.007
Response to stimulus GO:0050896 197 0.007
Cuticle development GO:0042335 9 0.009
Root development and morphogenesis GO:0010101, GO:0010015, GO:0010311, GO:0022411, GO:0048528 30 0.01
Cellular response to sucrose starvation, mannitol and sorbitol GO:0018008, GO:0018201, GO:0043617, GO:0071325, GO:0072709 3 0.012
Organic acid biosynthesis GO:0016053, GO:0046394, GO:0072330 50 0.041
Leaves description: molecular functions   
Xyloglucan:xyloglucosyl transferase activity GO:0016762 11 0
Transferase activity, transferring acyl groups GO:0016746 25 0
Tetrapyrrole binding GO:0046906 20 0.004
Oxidoreductase activity GO:0016491, GO:0016661, GO:0016701, GO:0016702 59 0.029
Phosphatidylinositol binding GO:0005547, GO:0043325 2 0.033
Carboxylic ester hydrolase activity GO:0052689 18 0.033
Catalytic activity GO:0003824 209 0.041
Roots description: biological processes GO Terms DEGs P -value
Cell junction organization and assembly GO:0034329, GO:0034330 12 0
Root development GO:0009913, GO:0010053, GO:0022622, GO:0048364, GO:0048640 40 0
Response to ethylene and other stimuli GO:0050896, GO:0070887, GO:0071369 198 0
Phenylpropanoid biosynthesis and metabolism GO:0009698, GO:0009699, GO:0009812, GO:0009813, GO:0009962, GO:0009963, GO:0043455, GO:1900376, GO:1900378, GO:2000762 27 0.002
Response to oxidative and other stress GO:0006950, GO:0006979 155 0.002
Zinc ion transmembrane transport GO:0006829, GO:0071577 6 0.003
Steroid biosynthesis and metabolism GO:0006694, GO:0008202 16 0.009
Coumarin biosynthesis and metabolism GO:0009804, GO:0009805 9 0.015
N-terminal peptidyl-glycine N-myristoylation GO:0018008 2 0.021
Immune system process GO:0002376 45 0.027
Cellular response to starvation GO:0009267 23 0.03
Single-organism biosynthesis and metabolism GO:0044710, GO:0044711 140 0.036
Cellular amine metabolic process GO:0044106 12 0.038
Cell wall organization or biogenesis GO:0071554 44 0.039
Cell communication GO:0007154 85 0.044
Roots description: molecular functions   
Antioxidant activity GO:0016209, GO:0016684 22 0
Tetrapyrrole binding GO:0046906 26 0
Oxidoreductase activity GO:0016491 58 0.002
Protein homodimerization activity GO:0042803 13 0.002
Zinc ion transmembrane transporter activity GO:0005385 6 0.002
Regulatory region nucleic acid binding GO:0001067 32 0.003
ADP binding GO:0043531 17 0.005
Identical protein binding GO:0042802 16 0.005
  1. To determine gene ontology terms overrepresented among differentially expressed genes in leaves or roots, Ontologizer 2.0 software [50] was used with parent–child-union analysis and Westfall-Young-Single-Step multiple testing correction, with a resampling of 1000 replicates. GO terms were combined when Glyma IDs overlapped entirely between two or more terms. The term containing the largest number of genes is in bold, with its corresponding P-value reported.
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