Skip to main content

Table 2 Characteristics of significant GO-ontology groups before (all rows) and after REViGO calculation (marked in bold)

From: Analysis of transcriptomic differences between NK603 maize and near-isogenic varieties using RNA sequencing and RT-qPCR

GO:ID

Description

No. genes AG8025 vs AG8025RR2

No. genes AG9045 AG9045RR2

No. of common genes

SEA_FDR mv

log10_p-val

Frequency (%)

Uniquen

Dispens

GO:0003006

development process involved in reproduction

350

71

22

0.0310

−1.5086

1.227

0.92

0.00

GO:0042221

Response to chemical

726

150

42

0.0000

−4.4909

4.749

0.34

0.00

GO:0044711

Single-organism biosynthetic process

534

91

24

0.0160

−1.7959

6.613

0.87

0.00

GO:0044763

Single-organism cellular process

1398

238

67

0.0177

−1.7533

19.396

0.87

0.3

GO:0009651

Response to salt stress

178

40

14

0.0024

−2.6289

0.389

0.37

0.41

GO:0009266

Response to temperature stimulus

167

43

10

0.0020

−2.6946

0.601

0.37

0.74

GO:0006970

Response to osmotic stress

186

46

15

0.0016

−2.7945

0.468

0.36

0.71

GO:0044710

Single-organism metabolic process

1112

181

51

0.0210

−1.6778

23.696

0.87

0.42

GO:0051707

Response to other organism

293

63

17

0.0014

−2.8697

0.704

0.33

0.44

GO:0043207

Response to external biotic stimulus

294

64

17

0.0014

−2.8697

0.704

0.33

0.97

GO:0009620

Response to fungus

120

26

9

0.0137

−1.8649

0.285

0.36

0.91

GO:0098542

Defense response to other organism

120

26

9

0.0083

−2.0835

0.601

0.31

0.98

GO:0009607

Response to biotic stimulus

311

66

17

0.0019

−2.7328

0.771

0.42

0.44

GO:0009605

Response to external stimulus

423

82

24

0.0011

−2.9788

1.057

0.41

0.46

GO:1901700

Response to oxygen-containing compound

428

101

29

0.0006

−3.2217

1.196

0.35

0.47

GO:0010033

Response to organic substance

519

121

36

0.0010

−3.0222

2.423

0.31

0.71

GO:0070887

Cellular response to chemical stimulus

349

76

16

0.0186

−1.7317

1.470

0.34

0.73

GO:0006952

Defense response

330

64

15

0.0036

−2.4461

1.312

0.37

0.48

GO:0009628

Response to abiotic stimulus

462

109

25

0.0004

−3.4144

1.925

0.38

0.5

GO:0009719

Response to endogenous stimulus

388

95

27

0.0125

−1.9031

2.168

0.38

0.51

GO:0010035

Response to inorganic substance

261

52

14

0.0108

−1.9666

0.735

0.37

0.62

GO:0006950

Response to stress

821

146

39

0.0077

−2.1135

7.803

0.31

0.62

GO:0001101

Response to acid chemical

290

71

19

0.0075

−2.1240

0.753

0.37

0.62

GO:0009409

Response to cold

125

30

8

0.0031

−2.5157

0.310

0.38

0.68

  1. GO:ID, identity of GO-Ontologies; description, definition of ontologies; nr.genes AG8025 vs AG8025RR2, and nr.genes AG9045 vs AG9045RR2, number of genes in the ontology groups AG8025 vs AG8025RR2, and AG9045 vs AG9045RR2; common genes(nr.), number of genes commonly up- or downregulated genes in both variety pairs; SEA_FDR mv, mean value of AG8025 and AG9045 false discovery rate (p < 0.05); Rev log10, log10 value of REViGO analysis; Frequ, proportion of GO terms in the annotation database; Uniqueness, comparison measure to other ontologies (Parameter for ontology outliers); Dispensability, similarity threshold for elimination of ontologies