Table 5

Gene Ontology terms enriched in up- and down-regulated genes

GO IDa

GO category name

Genes in genomeb

Genes in subsetc

P-valued


Up-regulated at 8 h encystation (compared to trophozoite)

GO:0006030

Chitin metabolism

5

5

1.21 × 10-7

GO:0006041

Glucosamine metabolism

5

5

1.21 × 10-7

GO:0006807

Nitrogen compound metabolism

33

7

3.33 × 10-4

GO:0009308

Amine metabolism

27

6

6.94 × 10-4

GO:0005975

Carbohydrate metabolism

115

11

7.92 × 10-3

GO:0001522

Pseudouridine synthesis

7

3

2.23 × 10-3

GO:0007017

Microtubule-based process

13

4

1.57 × 10-3

Up-regulated at 24 h encystation (compared to trophozoite)

GO:0006030

Chitin metabolism

5

3

4.10 × 10-3

GO:0006807

Nitrogen compound metabolism

33

7

1.15 × 10-2

GO:0009308

Amine metabolism

27

6

1.52 × 10-2

GO:0016311

Dephosphorylation

54

9

2.13 × 10-2

GO:0006351

Transcription, DNA-dependent

35

6

4.96 × 10-2

GO:0006367

Transcription initiation from RNA polymerase II promoter

11

3

4.78 × 10-2

GO:0007017

Microtubule-based process

13

6

2.22 × 10-4

GO:0007018

Microtubule-based movement

6

3

7.74 × 10-3

Up-regulated at 72 h encystation (compared to trophozoite)

GO:0009966

Regulation of signal transduction

120

13

7.62 × 10-3

GO:0007275

Development

10

3

1.22 × 10-2

GO:0040029

Regulation of gene expression, epigenetic

8

3

6.14 × 10-3

GO:0006139

Nucleobase, nucleoside, nucleotide and nucleic acid metabolism

328

24

4.39 × 10-2

GO:0051056

Regulation of small GTPase mediated

signal transduction

120

13

7.62 × 10-3

GO:0007017

Microtubule-based process

13

3

2.59 × 10-2

Up-regulated at 2 h excystation (compared to 72 h cyst)

GO:0019318

Hexose metabolism

21

8

9.38 × 10-4

GO:0005975

Carbohydrate metabolism

115

23

2.00 × 10-3

GO:0044262

Cellular carbohydrate metabolism

35

10

2.79 × 10-3

GO:0006096

Glycolysis

7

4

3.51 × 10-3

GO:0006007

Glucose catabolism

8

4

6.42 × 10-3

GO:0006006

Glucose metabolism

17

6

6.47 × 10-3

GO:0006066

Alcohol metabolism

28

8

7.31 × 10-3

GO:0051186

Cofactor metabolism

54

12

1.02 × 10-2

GO:0016052

Carbohydrate catabolism

10

4

1.62 × 10-2

GO:0016226

Iron-sulfur cluster assembly

7

4

3.51 × 10-2

GO:0042254

Ribosome biogenesis and assembly

18

5

3.65 × 10-2

GO:0008654

Phospholipid biosynthesis

14

5

1.22 × 10-2

GO:0046467

Membrane lipid biosynthesis

14

5

1.22 × 10-2

GO:0006644

Phospholipid metabolism

25

7

1.34 × 10-2

GO:0006497

Protein lipidation

10

4

1.62 × 10-2

GO:0006508

Proteolysis

138

25

5.27 × 10-3

GO:0006996

Organelle organization and biogenesis

112

21

6.85 × 10-3

GO:0006800

Oxygen and reactive oxygen species metabolism

5

3

1.04 × 10-2

Up-regulated at 8 h excystation (compared to 72 h cyst)

GO:0006066

Alcohol metabolism

28

8

1.26 × 10-2

GO:0005975

Carbohydrate metabolism

115

22

1.30 × 10-2

GO:0019752

Carboxylic acid metabolism

26

8

7.82 × 10-3

GO:0009059

Macromolecule biosynthesis

202

34

1.72 × 10-2

GO:0006260

DNA replication

56

12

2.65 × 10-2

GO:0006139

Nucleobase, nucleoside, nucleotide and nucleic acid metabolism

328

50

2.69 × 10-2

GO:0006259

DNA metabolism

144

25

2.71 × 10-2

GO:0016568

Chromatin modification

11

4

3.17 × 10-2

GO:0006629

Lipid metabolism

71

19

3.61 × 10-4

GO:0008610

Lipid biosynthesis

21

7

7.88 × 10-3

GO:0044255

Cellular lipid metabolism

38

10

1.02 × 10-2

GO:0008654

Phospholipid biosynthesis

14

5

1.78 × 10-2

GO:0006644

Phospholipid metabolism

25

7

2.15 × 10-2

GO:0006497

Protein lipidation

10

4

2.22 × 10-2

GO:0006508

Proteolysis

138

25

1.65 × 10-2

GO:0006996

Organelle organization and biogenesis

112

21

1.87 × 10-2

Down-regulated at 8 h encystation (compared to trophozoite)

GO:0009309

Amine biosynthesis

10

3

1.38 × 10-3

GO:0006519

Amino acid and derivative metabolism

23

4

1.86 × 10-3

GO:0005975

Carbohydrate metabolism

115

8

5.37 × 10-3

GO:0019752

Carboxylic acid metabolism

26

3

2.27 × 10-2

GO:0051186

Cofactor metabolism

54

4

3.81 × 10-2

GO:0016226

Iron-sulfur cluster assembly

7

4

9.80 × 10-6

GO:0050896

Response to stimulus

46

4

3.14 × 10-2

GO:0006323

DNA packaging

39

4

1.81 × 10-2

GO:0051276

Chromosome organization and biogenesis

43

4

2.52 × 10-2

GO:0006259

DNA metabolism

144

8

3.36 × 10-2

GO:0046467

Membrane lipid biosynthesis

14

3

3.90 × 10-3

GO:0006644

Phospholipid metabolism

25

3

2.04 × 10-2

GO:0006497

Protein lipidation

10

3

1.38 × 10-3

Down-regulated at 24 h encystation (compared to trophozoite)

GO:0005975

Carbohydrate metabolism

115

7

2.99 × 10-2

GO:0050896

Response to stimulus

46

4

3.14 × 10-2

GO:0006323

DNA packaging

39

4

1.81 × 10-2

GO:0051276

Chromosome organization and biogenesis

43

4

2.52 × 10-2

GO:0006259

DNA metabolism

144

8

3.36 × 10-2

GO:0031497

Chromatin assembly

30

3

4.27 × 10-2

GO:0006461

Protein complex assembly

31

3

4.64 × 10-2

Down-regulated at 72 h encystation (compared to trophozoite)

GO:0006096

Glycolysis

7

5

2.22 × 10-4

GO:0019320

Hexose catabolism

8

5

5.42 × 10-4

GO:0046365

Monosaccharide catabolism

8

5

5.42 × 10-4

GO:0006007

Glucose catabolism

8

5

5.42 × 10-4

GO:0005996

Monosaccharide metabolism

22

8

1.19 × 10-3

GO:0005975

Carbohydrate metabolism

115

23

1.58 × 10-3

GO:0006092

Main pathways of carbohydrate metabolism

12

5

5.35 × 10-3

GO:0016052

Carbohydrate catabolism

10

5

2.04 × 10-3

GO:0016226

Iron-sulfur cluster assembly

7

4

3.28 × 10-3

GO:0031163

Metallo-sulfur cluster assembly

7

4

3.28 × 10-3

GO:0006629

Lipid metabolism

71

15

5.95 × 10-3

GO:0051258

Protein polymerization

4

3

4.29 × 10-3

GO:0030036

Actin cytoskeleton organization and biogenesis

7

4

3.28 × 10-3

GO:0030041

Actin filament polymerization

4

3

4.29 × 10-3

GO:0008154

Actin polymerization and/or depolymerization

4

3

4.29 × 10-3

GO:0016043

Cell organization and biogenesis

306

51

3.70 × 10-4

GO:0006996

Organelle organization and biogenesis

112

21

5.58 × 10-3

GO:0006800

Oxygen and reactive oxygen species metabolism

5

4

5.58 × 10-4

GO:0006801

Superoxide metabolism

5

4

5.58 × 10-4

Down-regulated at 2 h excystation (compared to 72 h cyst)

GO:0007154

Cell communication

566

23

3.73 × 10-2

GO:0016043

Cell organization and biogenesis

306

14

4.47 × 10-2

Down-regulated at 8 h excystation (compared to 72 h cyst)

GO:0008643

Carbohydrate transport

5

3

3.56 × 10-3

GO:0044249

Cellular biosynthesis

276

51

1.18 × 10-10

GO:0006412

Protein biosynthesis

194

44

2.14 × 10-12

GO:0006414

Translational elongation

11

3

4.21 × 10-2

GO:0051276

Chromosome organization and biogenesis

43

9

3.42 × 10-3

GO:0006323

DNA packaging

39

8

6.49 × 10-3

GO:0031497

Chromatin assembly

30

6

2.01 × 10-2

GO:0006334

Nucleosome assembly

23

6

5.27 × 10-3

GO:0006461

Protein complex assembly

31

7

6.20 × 10-3

GO:0016043

Cell organization and biogenesis

306

32

2.40 × 10-2

GO:0006996

Organelle organization and biogenesis

112

14

3.41 × 10-2


aSelected GO terms that were significantly enriched (P < 0.05) in genes up- or down-regulated at 8 h, 24 h and 72 h post-encystation, and at 2 h post-excystation. bNumber of genes in a GO category in the whole E. invadens genome. cNumber of genes in a GO category among the subset of regulated genes. dP-value for GO category enrichment.

Ehrenkaufer et al. Genome Biology 2013 14:R77   doi:10.1186/gb-2013-14-7-r77

Open Data