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Table 2 Gene ontology analysis of 972 up-regulated genes

From: Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid

GO ID GO term Query item Background item FDR p-value
  biological process  
Regulation of biological process
regulation of metabolic process
GO:0080090 regulation of primary metabolic process 53 324 8.30E-30
GO:0045449 regulation of transcription 51 321 3.00E-28
GO:0060255 regulation of macromolecule metabolic process 53 326 1.10E-29
GO:0010556 regulation of macromolecule biosynthetic process 52 322 4.40E-29
GO:0010468 regulation of gene expression 52 324 5.50E-29
GO:0009889 regulation of biosynthetic process 52 322 4.40E-29
GO:0051171 regulation of nitrogen compound metabolic process 51 323 3.90E-28
regulation of cellular process     
GO:0007165 signal transduction 11 106 6.30E-05
GO:0007242 intracellular signaling cascade 10 68 6.90E-06
Biological regulation     
GO:0065008 regulation of biological quality 12 14 4.40E-18
Multi-organism process     
GO:0051707 response to other organism 9 39 4.80E-07
GO:0009617 response to bacterium 6 7 3.80E-09
Cellular process     
cellular response to stimulus     
GO:0070887 cellular response to chemical stimulus 7 43 0.00013
GO:0055085 transmembrane transport 9 12 1.10E-12
Metabolic process     
primary metabolic process     
GO:0005975 carbohydrate metabolic process 37 138 3.60E-29
GO:0005976 polysaccharide metabolic process 12 57 1.10E-08
GO:0006022 aminoglycan metabolic process 6 21 1.70E-05
GO:0006030 chitin metabolic process 6 21 1.70E-05
GO:0016052 carbohydrate catabolic process 17 45 1.10E-16
GO:0006629 lipid metabolic process 21 81 1.20E-16
GO:0019538 protein metabolic process 80 487 4.30E-44
GO:0006508 proteolysis 23 126 1.30E-14
secondary metabolic process     
GO:0006721 terpenoid metabolic process 5 54 0.025
GO:0016101 diterpenoid metabolic process 5 35 0.0036
GO:0009698 phenylpropanoid metabolic process 6 11 2.10E-07
macromolecule metabolic process     
GO:0019538 protein metabolic process 80 487 4.30E-44
GO:0043412 macromolecule modification 50 265 3.60E-31
GO:0006464 protein modification process 50 264 3.10E-31
GO:0044036 cell wall macromolecule metabolic process 11 21 6.10E-13
GO:0016998 cell wall macromolecule catabolic process 7 21 8.60E-07
GO:0010467 gene expression 55 419 3.50E-26
GO:0009059 macromolecule biosynthetic process 56 569 1.30E-20
Establishment of localization     
transport     
GO:0006811 ion transport 13 66 5.40E-09
GO:0006812 cation transport 10 65 4.60E-06
GO:0030001 metal ion transport 10 36 1.30E-08
Response to stimulus     
GO:0009719 response to endogenous stimulus 8 106 0.0075
GO:0009628 response to abiotic stimulus 7 41 9.70E-05
GO:0009607 response to biotic stimulus 13 39 4.10E-12
GO:0006950 response to stress 46 103 2.00E-47
GO:0006952 defense response 16 59 3.40E-13
GO:0006979 response to oxidative stress 11 17 2.40E-14
GO:0042221 response to chemical stimulus 27 133 3.00E-18
GO:0010033 response to organic substance 8 106 0.0075
  molecular function  
Molecular transducer activity     
GO:0004871 signal transducer activity 13 32 2.00E-13
Transporter activity     
substrate-specific transporter activity     
GO:0022891 substrate-specific transmembrane transporter 14 79 4.90E-09
GO:0015075 ion transmembrane transporter activity 9 68 5.20E-05
GO:0008324 cation transmembrane transporter activity 5 62 0.04
transmembrane transporter activity     
GO:0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 5 17 9.30E-05
GO:0042626 ATPase activity, coupled to transmembrane movement of substances 5 17 9.30E-05
active transmembrane transporter activity     
GO:0015291 secondary active transmembrane transporter 7 24 2.20E-06
GO:0015399 primary active transmembrane transporter activity 5 25 0.00064
Antioxidant activity     
GO:0004601 peroxidase activity 8 68 0.00036
Transcription regulator activity     
GO:0003700 transcription factor activity 26 116 9.00E-19
Catalytic activity     
oxidoreductase activity     
GO:0004497 monooxygenase activity 21 47 2.40E-22
GO:0051213 dioxygenase activity 7 7 1.10E-11
GO:0015036 disulfide oxidoreductase activity 7 10 1.20E-09
transferase activity     
GO:0016757 transferase activity, transferring glycosyl groups 24 31 1.00E-33
GO:0016758 transferase activity, transferring hexosyl groups 19 30 3.70E-24
GO:0016772 transferase activity, transferring phosphorus-containing groups 54 426 5.10E-25
GO:0016773 phosphotransferase activity, alcohol group as 47 244 6.30E-30
GO:0004672 protein kinase activity 42 235 1.40E-25
GO:0016301 kinase activity 51 261 1.10E-32
hydrolase activity     
GO:0016798 hydrolase activity, acting on glycosyl bonds 25 87 6.40E-21
GO:0004553 hydrolase activity, hydrolyzing O-glycosy 24 85 6.50E-20
GO:0004568 chitinase activity 9 21 1.00E-09
Binding     
carbohydrate binding     
GO:0005529 sugar binding 6 10 9.10E-08
nucleic acid binding     
ion binding     
GO:0043169 cation binding 126 175 6.50E-166
GO:0046872 metal ion binding 111 173 1.60E-137
GO:0046914 transition metal ion binding 80 132 9.80E-97
GO:0008270 zinc ion binding 30 89 3.60E-27
GO:0005507 copper ion binding 6 19 9.00E-06
GO:0005509 calcium ion binding 20 39 7.80E-23