Table 4

Average incoming connectivity for the Gene Ontology pathways from all levels in A. thaliana

GO pathways*

Number of genes

Number of TFs^†

Number of TF/Number of genes^‡

Number of FFLs^§

Top five with the highest total number of TFs

Response to other organisms

296

2,249

7.6

9,865

Secondary metabolic process

284

1,964

6.9

3,321

Response to temperature stimulus

238

1,650

6.9

10,151

Anatomical structure morphogenesis

291

1,537

5.3

13,275

Response to radiation

250

1,524

6.1

6,233

Top five with the lowest total number of TFs

Glycerophospholipid metabolic process

21

38

1.8

69

Sulfur amino acid biosynthetic process

24

60

2.5

13

Gametophyte development

24

62

2.6

1

Cellular morphogenesis in differentiation

25

68

2.7

78

Indole and derivative metabolic process

22

71

3.2

46

Top five with the highest relative number of TFs

Defense response to fungus

26

355

13.7

4,353

Photosynthesis

80

1,064

13.3

2,459

Response to light intensity

26

334

12.8

2,652

Chlorophyll biosynthetic process

22

243

11.0

443

Porphyrin biosynthetic process

39

421

10.8

754

Top five with the lowest relative number of TFs

Glycerophospolipic metabolic process

21

38

1.8

0

Membrane lipid biosynthetic process

48

111

2.3

121

Sulfur compound biosynthetic process

32

75

2.3

98

Golgi vesicle transport

44

104

2.4

47

Biogenic amine metabolic process

32

76

2.4

53

*Only GO pathways involving more than 20 genes and less than 300 from all levels were selected. ^†Total number of TFs that regulate the genes of the GO pathway. ^‡Relative number of TFs. ^§Total number of FFLs involved in the GO pathway.

Carrera et al. Genome Biology 2009 10:R96   doi:10.1186/gb-2009-10-9-r96