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Table 3 Gene Ontology (GO) terms enriched in significant proteins after repetitive somatic embryogenesis in Douglas-fir

From: Repetitive somatic embryogenesis induced cytological and proteomic changes in embryogenic lines of Pseudotsuga menziesii [Mirb.]

GO.ID

Term

Annot.

Sign.

Exp.

ratio sign./exp.

Expression

Secondary versus primary lines

 GO:0015977

carbon fixation

17

2

0.13

15.38

2ry > 1ry

 GO:0009269

response to desiccation

17

2

0.13

15.38

2ry > 1ry

 GO:0006099

tricarboxylic acid cycle

38

2

0.28

7.14

2ry > 1ry

 GO:0015979

photosynthesis

43

2

0.32

6.25

2ry > 1ry

 GO:0051603

proteolysis involved in cellular protein catabolic process

142

5

1.05

4.76

2ry > 1ry

 GO:0043488

regulation of mRNA stability

2

2

0.05

40.00

1ry > 2ry

 GO:0046292

formaldehyde metabolic process

4

2

0.1

20.00

1ry > 2ry

 GO:0006556

S-adenosylmethionine biosynthetic process

7

3

0.18

16.67

1ry > 2ry

 GO:0006097

glyoxylate cycle

7

3

0.18

16.67

1ry > 2ry

 GO:0010030

positive regulation of seed germination

5

2

0.13

15.38

1ry > 2ry

 GO:0051262

protein tetramerization

6

2

0.15

13.33

1ry > 2ry

 GO:1901663

quinone biosynthetic process

13

4

0.33

12.12

1ry > 2ry

 GO:0006558

L-phenylalanine metabolic process

15

4

0.38

10.53

1ry > 2ry

 GO:0009969

xyloglucan biosynthetic process

8

2

0.2

10.00

1ry > 2ry

 GO:0009051

pentose-phosphate shunt, oxidative branch

8

2

0.2

10.00

1ry > 2ry

 GO:0042593

glucose homeostasis

8

2

0.2

10.00

1ry > 2ry

 GO:0010262

somatic embryogenesis

14

3

0.35

8.57

1ry > 2ry

 GO:0006032

chitin catabolic process

22

4

0.55

7.27

1ry > 2ry

 GO:0009813

flavonoid biosynthetic process

58

9

1.46

6.16

1ry > 2ry

 GO:0002215

defense response to nematode

13

2

0.33

6.06

1ry > 2ry

 GO:0006730

one-carbon metabolic process

27

4

0.68

5.88

1ry > 2ry

 GO:0080167

response to karrikin

44

6

1.11

5.41

1ry > 2ry

 GO:0009699

phenylpropanoid biosynthetic process

93

12

2.34

5.13

1ry > 2ry

 GO:0008219

cell death

77

9

1.94

4.64

1ry > 2ry

 GO:0016998

cell wall macromolecule catabolic process

26

3

0.65

4.62

1ry > 2ry

 GO:0006555

methionine metabolic process

28

3

0.71

4.23

1ry > 2ry

 GO:0009611

response to wounding

129

13

3.25

4.00

1ry > 2ry

 GO:0009787

regulation of abscisic acid-activated signaling pathway

30

3

0.76

3.95

1ry > 2ry

 GO:0009411

response to UV

53

5

1.33

3.76

1ry > 2ry

 GO:0009808

lignin metabolic process

85

8

2.14

3.74

1ry > 2ry

 GO:0000272

polysaccharide catabolic process

64

6

1.61

3.73

1ry > 2ry

 GO:0009626

plant-type hypersensitive response

44

4

1.11

3.60

1ry > 2ry

 GO:0009636

response to toxic substance

49

4

1.23

3.25

1ry > 2ry

 GO:0031408

oxylipin biosynthetic process

51

4

1.28

3.13

1ry > 2ry

 GO:0055114

oxidation-reduction process

684

36

17.22

2.09

1ry > 2ry

Tertiary versus secondary lines

 GO:0006433

prolyl-tRNA aminoacylation

2

2

0.06

33.33

3ry > 2ry

 GO:0009871

jasmonic acid and ethylene-dependent systemic resistance. Ethylene mediated signaling pathway

5

3

0.16

18.75

3ry > 2ry

 GO:0009969

xyloglucan biosynthetic process

8

3

0.26

11.54

3ry > 2ry

 GO:0031640

killing of cells of other organism

11

4

0.35

11.43

3ry > 2ry

 GO:0010731

protein glutathionylation

7

2

0.22

9.09

3ry > 2ry

 GO:0010183

pollen tube guidance

14

4

0.45

8.89

3ry > 2ry

 GO:0006558

L-phenylalanine metabolic process

15

4

0.48

8.33

3ry > 2ry

 GO:0046487

glyoxylate metabolic process

8

2

0.26

7.69

3ry > 2ry

 GO:0080092

regulation of pollen tube growth

17

4

0.54

7.41

3ry > 2ry

 GO:0043650

dicarboxylic acid biosynthetic process

13

3

0.41

7.32

3ry > 2ry

 GO:0006032

chitin catabolic process

22

5

0.7

7.14

3ry > 2ry

 GO:0046189

phenol-containing compound biosynthetic process

9

2

0.29

6.90

3ry > 2ry

 GO:0006949

syncytium formation

9

2

0.29

6.90

3ry > 2ry

 GO:0080167

response to karrikin

44

8

1.4

5.71

3ry > 2ry

 GO:0006816

calcium ion transport

11

2

0.35

5.71

3ry > 2ry

 GO:0009828

plant-type cell wall loosening

11

2

0.35

5.71

3ry > 2ry

 GO:0009626

plant-type hypersensitive response

44

7

1.4

5.00

3ry > 2ry

 GO:0000272

polysaccharide catabolic process

64

10

2.04

4.90

3ry > 2ry

 GO:0072329

monocarboxylic acid catabolic process

42

6

1.34

4.48

3ry > 2ry

 GO:0006749

glutathione metabolic process

56

8

1.79

4.47

3ry > 2ry

 GO:0031408

oxylipin biosynthetic process

51

7

1.63

4.29

3ry > 2ry

 GO:0009718

anthocyanin-containing compound biosynthetic process

23

3

0.73

4.11

3ry > 2ry

 GO:0019395

fatty acid oxidation

39

5

1.24

4.03

3ry > 2ry

 GO:0009611

response to wounding

129

15

4.11

3.65

3ry > 2ry

 GO:0050832

defense response to fungus

102

11

3.25

3.38

3ry > 2ry

 GO:0009699

phenylpropanoid biosynthetic process

93

10

2.96

3.38

3ry > 2ry

 GO:0009808

lignin metabolic process

85

9

2.71

3.32

3ry > 2ry

 GO:0006952

defense response

370

31

11.79

2.63

3ry > 2ry

 GO:0044248

cellular catabolic process

472

39

15.05

2.59

3ry > 2ry

 GO:0006979

response to oxidative stress

232

16

7.4

2.16

3ry > 2ry

 GO:0009617

response to bacterium

201

13

6.41

2.03

3ry > 2ry

 GO:0055114

oxidation-reduction process

684

44

21.8

2.02

3ry > 2ry

 GO:0051603

proteolysis involved in cellular protein catabolic process

142

9

4.53

1.99

3ry > 2ry

 GO:0005975

carbohydrate metabolic process

414

24

13.2

1.82

3ry > 2ry

 GO:0010038

response to metal ion

393

19

12.53

1.52

3ry > 2ry

 GO:0006879

cellular iron ion homeostasis

3

2

0.03

66.67

2ry > 3ry

 GO:0010197

polar nucleus fusion

8

2

0.09

22.22

2ry > 3ry

 GO:0046274

lignin catabolic process

16

2

0.18

11.11

2ry > 3ry

 GO:0048509

regulation of meristem development

20

2

0.23

8.70

2ry > 3ry

 GO:0010051

xylem and phloem pattern formation

24

2

0.27

7.41

2ry > 3ry

 GO:0000398

mRNA splicing. Via spliceosome

56

4

0.63

6.35

2ry > 3ry

 GO:0016310

phosphorylation

222

6

2.51

2.39

2ry > 3ry

 GO:0032774

RNA biosynthetic process

262

7

2.97

2.36

2ry > 3ry

  1. GO.ID: Gene Ontology Identifiant; Annot.: number of annotated Douglas proteins with GO terms in the data set; Sign.: number of Douglas proteins in the analysed dataset; Exp.: expected number of interesting proteins mapped to the GO term if randomly distributed over all GO terms; ratio sign./exp: ratio between significant and expected proteins mapping to the GO term; Expression: proteins assigned to specific GO term are over-expressed in 1ry (1ry > 2ry), 2ry (2ry > 1ry) or 3ry lines (3ry > 2ry). Only results with pvalue < 0.05 of the Fisher’s exact test were considered