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Table 2 Significantly enriched GO terms (Biological Process Ontology) in the subsets of differentially expressed genes (p-value < 0.05)

From: Transcriptional reprogramming caused by the geminivirus Tomato yellow leaf curl virus in local or systemic infections in Nicotiana benthamiana

GO.ID

Term

Annotated

Significant

Expected

p-value

Overrepresented in the subset of up-regulated in local infection

 GO:0006351

transcription, DNA-templated

2046

271

151.48

1.8E-22

 GO:0006310

DNA recombination

47

15

3.48

2.5E-06

 GO:0005992

trehalose biosynthetic process

34

12

2.52

3.1E-06

 GO:0048544

recognition of pollen

69

16

5.11

0.000034

 GO:0006302

double-strand break repair

16

7

1.18

0.000076

 GO:0006464

cellular protein modification process

2490

237

184.35

0.00008

 GO:0006012

galactose metabolic process

23

8

1.7

0.00016

 GO:0006950

response to stress

873

108

64.63

0.00022

 GO:0016310

phosphorylation

2148

196

159.03

0.00023

 GO:0006376

mRNA splice site selection

6

4

0.44

0.0004

 GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

3

3

0.22

0.00041

 GO:0006887

exocytosis

72

14

5.33

0.00071

 GO:0006635

fatty acid beta-oxidation

7

4

0.52

0.00087

 GO:0006281

DNA repair

271

38

20.06

0.00415

 GO:0043562

cellular response to nitrogen levels

2

2

0.15

0.00548

 GO:0009744

response to sucrose

2

2

0.15

0.00548

 GO:0045454

cell redox homeostasis

229

28

16.95

0.00608

 GO:0008272

sulfate transport

31

7

2.3

0.00653

 GO:0000160

phosphorelay signal transduction system

102

15

7.55

0.00799

 GO:0006334

nucleosome assembly

59

10

4.37

0.01074

 GO:0009298

GDP-mannose biosynthetic process

7

3

0.52

0.0113

 GO:0070966

nuclear-transcribed mRNA catabolic process, no-go decay

3

2

0.22

0.01562

 GO:0070481

nuclear-transcribed mRNA catabolic process, non-stop decay

3

2

0.22

0.01562

 GO:0071025

RNA surveillance

3

2

0.22

0.01562

 GO:0015706

nitrate transport

3

2

0.22

0.01562

 GO:0010167

response to nitrate

3

2

0.22

0.01562

 GO:0007064

mitotic sister chromatid cohesion

8

3

0.59

0.01709

 GO:0006032

chitin catabolic process

31

6

2.3

0.02419

 GO:0035434

copper ion transmembrane transport

9

3

0.67

0.02425

 GO:0050832

defense response to fungus

4

2

0.3

0.02972

 GO:0042742

defense response to bacterium

4

2

0.3

0.02972

 GO:0007050

cell cycle arrest

10

3

0.74

0.03277

 GO:0006529

asparagine biosynthetic process

11

3

0.81

0.04263

 GO:0006020

inositol metabolic process

11

3

0.81

0.04263

Overrepresented in the subset of down-regulated in local infection

 GO:0009765

photosynthesis, light harvesting

74

61

12.92

1E-30

 GO:0007017

microtubule-based process

254

105

44.35

4.6E-19

 GO:0033014

tetrapyrrole biosynthetic process

53

32

9.25

3.3E-12

 GO:0015979

photosynthesis

387

169

67.57

4.9E-12

 GO:0000079

regulation of cyclin-dependent protein serine/threonine kinase activity

48

29

8.38

3.4E-11

 GO:0006270

DNA replication initiation

18

16

3.14

7.7E-11

 GO:0072330

monocarboxylic acid biosynthetic process

171

61

29.85

8.1E-09

 GO:0051258

protein polymerization

86

34

15.01

8.8E-09

 GO:0006546

glycine catabolic process

11

9

1.92

5.8E-06

 GO:0005975

carbohydrate metabolic process

1345

320

234.82

0.000013

 GO:0006073

cellular glucan metabolic process

142

56

24.79

0.000026

 GO:0006260

DNA replication

119

55

20.78

0.000027

 GO:0000910

cytokinesis

24

12

4.19

0.000033

 GO:0006629

lipid metabolic process

928

234

162.02

0.00028

 GO:0030244

cellulose biosynthetic process

62

22

10.82

0.00051

 GO:0000096

sulfur amino acid metabolic process

50

18

8.73

0.00084

 GO:0006656

phosphatidylcholine biosynthetic process

4

4

0.7

0.00093

 GO:0018160

peptidyl-pyrromethane cofactor linkage

4

4

0.7

0.00093

 GO:1901070

guanosine-containing compound biosynthetic process

17

9

2.97

0.00094

 GO:0006418

tRNA aminoacylation for protein translation

95

29

16.59

0.00125

 GO:0009132

nucleoside diphosphate metabolic process

135

40

23.57

0.00155

 GO:0006228

UTP biosynthetic process

15

8

2.62

0.00171

 GO:0006241

CTP biosynthetic process

15

8

2.62

0.00171

 GO:0006269

DNA replication, synthesis of RNA primer

5

4

0.87

0.00399

 GO:0045132

meiotic chromosome segregation

5

4

0.87

0.00399

 GO:0009084

glutamine family amino acid biosynthetic process

31

12

5.41

0.00416

 GO:1901617

organic hydroxy compound biosynthetic process

23

14

4.02

0.00531

 GO:0009234

menaquinone biosynthetic process

3

3

0.52

0.00532

 GO:0016117

carotenoid biosynthetic process

14

7

2.44

0.00536

 GO:0009065

glutamine family amino acid catabolic process

12

6

2.1

0.00997

 GO:0046168

glycerol-3-phosphate catabolic process

6

4

1.05

0.01031

 GO:0015671

oxygen transport

6

4

1.05

0.01031

 GO:0006801

superoxide metabolic process

23

9

4.02

0.01161

 GO:0007076

mitotic chromosome condensation

13

6

2.27

0.01582

 GO:0006166

purine ribonucleoside salvage

4

3

0.7

0.01849

 GO:0006096

glycolytic process

114

29

19.9

0.02014

 GO:0046274

lignin catabolic process

33

11

5.76

0.02045

 GO:0042549

photosystem II stabilization

7

4

1.22

0.02075

 GO:0042026

protein refolding

14

6

2.44

0.02366

 GO:0019307

mannose biosynthetic process

2

2

0.35

0.03047

 GO:0007155

cell adhesion

2

2

0.35

0.03047

 GO:0045038

protein import into chloroplast thylakoid membrane

2

2

0.35

0.03047

 GO:0048478

replication fork protection

2

2

0.35

0.03047

 GO:0007623

circadian rhythm

2

2

0.35

0.03047

 GO:0010027

thylakoid membrane organization

2

2

0.35

0.03047

 GO:0006450

regulation of translational fidelity

2

2

0.35

0.03047

 GO:0030259

lipid glycosylation

15

6

2.62

0.03373

 GO:0009082

branched-chain amino acid biosynthetic process

23

8

4.02

0.03537

 GO:0006168

adenine salvage

5

3

0.87

0.04023

 GO:0010207

photosystem II assembly

5

3

0.87

0.04023

 GO:0006353

DNA-templated transcription, termination

5

3

0.87

0.04023

 GO:0006662

glycerol ether metabolic process

68

18

11.87

0.04094

Overrepresented in the subset of up-regulated in systemic infection

 GO:0006032

chitin catabolic process

31

7

0.78

9.1E-06

 GO:0006355

regulation of transcription, DNA-templated

1764

69

44.11

0.00012

 GO:0005975

carbohydrate metabolic process

1345

63

33.64

0.00022

 GO:0043562

cellular response to nitrogen levels

2

2

0.05

0.00062

 GO:0009744

response to sucrose

2

2

0.05

0.00062

 GO:0016998

cell wall macromolecule catabolic process

29

5

0.73

0.00069

 GO:0019310

inositol catabolic process

8

3

0.2

0.00079

 GO:0005992

trehalose biosynthetic process

34

5

0.85

0.00146

 GO:0015770

sucrose transport

3

2

0.08

0.00184

 GO:0019953

sexual reproduction

11

3

0.28

0.00221

 GO:0009607

response to biotic stimulus

43

6

1.08

0.00271

 GO:0006570

tyrosine metabolic process

5

2

0.13

0.00594

 GO:0006094

gluconeogenesis

8

2

0.2

0.01581

 GO:0006952

defense response

112

8

2.8

0.01862

 GO:0006541

glutamine metabolic process

23

3

0.58

0.01898

 GO:0000272

polysaccharide catabolic process

25

3

0.63

0.02376

 GO:0006662

glycerol ether metabolic process

68

5

1.7

0.02756

 GO:0003333

amino acid transmembrane transport

46

4

1.15

0.02758

 GO:0006529

asparagine biosynthetic process

11

2

0.28

0.02956

 GO:0008283

cell proliferation

11

2

0.28

0.02956

 GO:0044264

cellular polysaccharide metabolic process

148

7

3.7

0.03961

 GO:0008272

sulfate transport

31

3

0.78

0.04163

 GO:0006857

oligopeptide transport

33

3

0.83

0.04874

Overrepresented in the subset of down-regulated in systemic infection

 GO:0007018

microtubule-based movement

129

11

0.7

1.2E-10

 GO:0000079

regulation of cyclin-dependent protein serine/threonine kinase activity

48

7

0.26

7.2E-09

 GO:0007067

mitotic nuclear division

51

5

0.28

0.0001

 GO:0016114

terpenoid biosynthetic process

30

2

0.16

0.0116

 GO:0006265

DNA topological change

30

2

0.16

0.0116

 GO:0007094

mitotic spindle assembly checkpoint

3

1

0.02

0.0163

 GO:0006952

defense response

112

3

0.61

0.0235

 GO:0009813

flavonoid biosynthetic process

6

1

0.03

0.0323

 GO:0030244

cellulose biosynthetic process

62

2

0.34

0.0452

Overrepresented in the subset of up-regulated genes common to local and systemic infections

 GO:0043562

cellular response to nitrogen levels

2

2

0.01

0.000041

 GO:0009744

response to sucrose

2

2

0.01

0.000041

 GO:0005992

trehalose biosynthetic process

34

4

0.22

0.000066

 GO:0006094

gluconeogenesis

8

2

0.05

0.0011

 GO:0019310

inositol catabolic process

8

2

0.05

0.0011

 GO:0006529

asparagine biosynthetic process

11

2

0.07

0.0022

 GO:0006355

regulation of transcription, DNA-templated

1764

21

11.37

0.0043

 GO:0007205

protein kinase C-activating G-protein coupled receptor signaling pathway

24

2

0.15

0.0104

 GO:0006659

phosphatidylserine biosynthetic process

3

1

0.02

0.0192

 GO:0042742

defense response to bacterium

4

1

0.03

0.0255

 GO:0006562

proline catabolic process

4

1

0.03

0.0255

 GO:0050832

defense response to fungus

4

1

0.03

0.0255

 GO:0006570

tyrosine metabolic process

5

1

0.03

0.0318

 GO:0003333

amino acid transmembrane transport

46

2

0.3

0.0355

 GO:0009064

glutamine family amino acid metabolic process

57

3

0.37

0.0453

Overrepresented in the subset of down-regulated genes common to local and systemic infections

 GO:0007018

microtubule-based movement

129

10

0.43

1.4E-11

 GO:0000079

regulation of cyclin-dependent protein serine/threonine kinase activity

48

7

0.16

2.1E-10

 GO:0007067

mitotic nuclear division

51

5

0.17

0.000014

 GO:0006265

DNA topological change

30

2

0.1

0.0045

 GO:0007094

mitotic spindle assembly checkpoint

3

1

0.01

0.0099

 GO:0030244

cellulose biosynthetic process

62

2

0.21

0.0181

 GO:0006606

protein import into nucleus

12

1

0.04

0.0392