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Table 2 MAPPFinder results for genes significantly increased and significantly decreased in 12.5-day embryos versus adult mice

From: MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

GO name

Number changed

Number measured

Number in GO

% Changed

% Present

z score

Significantly increased

      

   Process

      

Mitotic cell cycle

44

70

89

62.9

78.7

8.1631

DNA metabolism

67

135

163

49.6

82.8

7.6807

mRNA splicing

19

21

30

90.5

70

7.4868

RNA processing

29

41

60

70.7

68.3

7.4411

RNA metabolism

30

44

66

68.2

66.7

7.3038

Cell cycle

98

240

291

40.8

82.5

7.0096

mRNA processing

24

33

45

72.7

73.3

6.9456

Protein biosynthesis

52

104

152

50

68.4

6.8095

Macromolecule biosynthesis

57

121

172

47.1

70.3

6.5863

DNA replication

28

46

55

60.9

83.6

6.2752

DNA replication and chromosome cycle

29

49

62

59.2

79

6.1944

Ribosome biogenesis

19

28

37

67.9

75.7

5.7749

Biosynthesis

89

242

334

36.8

72.5

5.4866

DNA dependent DNA replication

13

18

22

72.2

81.8

5.0697

Mitosis

13

18

24

72.2

75

5.0697

Nuclear division

14

21

30

66.7

70

4.8663

DNA packaging

20

36

46

55.6

78.3

4.7782

Cell organization and biogenesis

74

207

294

35.7

70.4

4.6913

M phase

15

25

36

60

69.4

4.5110

mRNA splice site selection

7

8

8

87.5

100

4.4125

DNA replication initiation

6

7

7

85.7

100

4.0138

Chromosome organization and biogenesis (sensu Eukarya)

18

37

51

48.6

72.5

3.8338

DNA repair

21

46

53

45.7

86.8

3.7895

Protein folding

12

22

31

54.5

71

3.6157

Cytoplasm organization and biogenesis

56

169

241

33.1

70.1

3.3912

Establishment and/or maintenance of chromatin architecture

13

27

35

48.1

77.1

3.2089

Protein synthesis elongation

6

9

37

66.7

24.3

3.1815

Chromatin assembly/disassembly

10

20

25

50

80

2.9585

Biological process unknown

34

98

250

34.7

39.2

2.9354

Protein-ligand dependent protein degradation

17

43

58

39.5

74.1

2.6968

Ubiquitin-dependent protein degradation

16

42

57

38.1

73.7

2.4404

Protein-nucleus import

5

9

10

55.6

90

2.3820

Ubiquitin cycle

6

12

16

50

75

2.2896

Nucleocytoplasmic transport

6

12

17

50

70.6

2.2896

Actin cytoskeleton organization and biogenesis

6

12

19

50

63.2

2.2896

Transmembrane receptor protein Ser/Thr kinase signaling pathway

10

25

31

40

80.6

2.1081

Induction of apoptosis

7

16

24

43.8

66.7

2.0449

   Component

      

Spliceosome

17

20

42

85

47.6

6.7175

Cytosolic ribosome (sensu Eukarya)

19

26

33

73.1

78.8

6.2032

Cytosol

40

85

112

47.1

75.9

5.4872

Ribosome

35

71

93

49.3

76.3

5.4624

Chromosome

19

36

55

52.8

65.5

4.3772

Nuclear envelope-endoplasmic reticulum network

9

12

17

75

70.6

4.3676

Adherens junction

6

7

14

85.7

50

4.0138

Endoplasmic reticulum membrane

7

9

13

77.8

69.2

3.9811

Chromatin

15

28

41

53.6

68.3

3.9579

Cellular component unknown

41

117

291

35

40.2

3.3057

Nucleolus

10

19

34

52.6

55.9

3.1587

26S proteasome

11

22

23

50

95.7

3.1036

Endoplasmic reticulum

39

117

141

33.3

83

2.8569

20S core proteasome

9

19

19

47.4

100

2.6078

Nuclear membrane

6

11

18

54.5

61.1

2.5536

Cytoskeleton

64

223

306

28.7

72.9

2.2918

Collagen

10

25

31

40

80.6

2.1081

Golgi membrane

7

16

18

43.8

88.9

2.0449

Actin cytoskeleton

16

46

63

34.8

73

2.0140

   Function

      

RNA binding

51

113

155

45.1

72.9

5.8498

Cyclin-dependent protein kinase

17

24

33

70.8

72.7

5.6944

Structural constituent of ribosome

39

83

101

47

82.2

5.4055

Cyclin-dependent protein kinase, regulator

12

17

24

70.6

70.8

4.7646

Structural molecule

77

223

278

34.5

80.2

4.4306

Pre-mRNA splicing factor

7

8

12

87.5

66.7

4.4125

mRNA binding

10

14

19

71.4

73.7

4.3979

Protein serine/threonine kinase

62

181

243

34.3

74.5

3.8821

Actin binding

25

58

83

43.1

69.9

3.7927

Proteasome endopeptidase

11

19

19

57.9

100

3.7096

DNA-directed DNA polymerase

7

10

15

70

66.7

3.6069

RHO small monomeric GTPase

7

10

10

70

100

3.6069

Nucleotidyltransferase

16

33

41

48.5

80.5

3.5964

Kinase regulator

15

33

42

45.5

78.6

3.1777

DNA dependent adenosinetriphosphatase

8

14

16

57.1

87.5

3.1151

Cytoskeletal protein binding

33

93

144

35.5

64.6

3.0423

DNA repair protein

11

23

27

47.8

85.2

2.9232

Translation factor, nucleic acid binding

14

32

43

43.8

74.4

2.8970

Transcription co-activator

6

10

14

60

71.4

2.8483

Chromatin binding

5

8

11

62.5

72.7

2.7166

Kinase

89

311

394

28.6

78.9

2.6983

Phosphotransferase, alcohol group as acceptor

87

305

386

28.5

79

2.6301

Protein kinase

76

263

336

28.9

78.3

2.5796

Exonuclease

6

11

15

54.5

73.3

2.5536

Small monomeric GTPase

15

38

46

39.5

82.6

2.5247

GTP binding

43

141

201

30.5

70.1

2.3248

Peptidylprolyl cis-trans isomerase

6

12

16

50

75

2.2896

Translation elongation factor

6

12

16

50

75

2.2896

Transcription factor binding

11

27

43

40.7

62.8

2.2838

Guanyl nucleotide binding

46

155

219

29.7

70.8

2.1927

Adenosinetriphosphatase

12

31

38

38.7

81.6

2.1763

Molecular_function unknown

29

91

230

31.9

39.6

2.1739

Protein binding

99

368

539

26.9

68.3

2.1328

Chaperone

16

45

62

35.6

72.6

2.1166

Extracellular matrix structural constituent conferring tensile strength

10

25

31

40

80.6

2.1081

DNA-directed RNA polymerase

5

10

11

50

90.9

2.0897

Structural constituent of cytoskeleton

21

63

79

33.3

79.7

2.0838

Transferase, transferring one-carbon groups

8

19

29

42.1

65.5

2.0570

GTPase

25

78

95

32.1

82.1

2.0488

Isomerase

12

32

42

37.5

76.2

2.0468

Significantly decreased

      

   Process

      

Fatty acid metabolism

19

30

41

63.3

73.2

5.9082

Main pathways of carbohydrate metabolism

20

39

50

51.3

78

4.8600

Energy derivation by oxidation of organic compounds

23

50

66

46

75.8

4.5739

Catabolic carbohydrate metabolism

18

36

45

50

80

4.4754

Tricarboxylic acid cycle

6

8

10

75

80

3.8664

Hexose metabolism

18

41

49

43.9

83.7

3.8016

Lipid metabolism

42

127

167

33.1

76

3.6708

Lipid transport

5

7

11

71.4

63.6

3.3807

Glycolysis

12

26

32

46.2

81.2

3.3091

Peroxisome organization and biogenesis

7

12

15

58.3

80

3.2972

Glucose metabolism

15

36

42

41.7

85.7

3.2247

Lymph gland development

8

15

17

53.3

88.2

3.2043

Cell proliferation

10

21

34

47.6

61.8

3.1400

Humoral immune response

15

37

79

40.5

46.8

3.0982

Carbohydrate metabolism

31

95

135

32.6

70.4

3.0557

Regulation of cell proliferation

5

8

15

62.5

53.3

2.9848

Muscle contraction

9

20

28

45

71.4

2.7716

Muscle development

13

34

43

38.2

79.1

2.6328

Mesoderm development

28

90

111

31.1

81.1

2.6096

Potassium transport

17

49

60

34.7

81.7

2.5450

Metal ion transport

24

77

100

31.2

77

2.4230

Monovalent inorganic cation transport

21

67

88

31.3

76.1

2.2935

Complement activation

8

20

23

40

87

2.2132

Cation transport

28

98

135

28.6

72.6

2.0923

Electron transport

25

87

113

28.7

77

2.0075

   Component

      

Mitochondrion

88

187

293

47.1

63.8

9.3508

Peroxisome

18

29

42

62.1

69

5.6381

Mitochondrial inner membrane

19

36

60

52.8

60

4.8922

Mitochondrial electron transport chain complex

10

14

32

71.4

43.8

4.7848

Mitochondrial membrane

20

40

72

50

55.6

4.7195

Cytochrome C oxidase

6

8

16

75

50

3.8664

Mitochondrial matrix

9

22

33

40.9

66.7

2.4283

Basement lamina

5

11

11

45.5

100

2.0910

Cytoskeleton

57

223

306

25.6

72.9

2.0527

   Function

      

Hydrogen ion transporter

11

15

33

73.3

45.5

5.1373

Primary active transporter

27

64

107

42.2

59.8

4.4175

Cation transporter

17

36

61

47.2

59

4.0585

Ion transporter

19

43

79

44.2

54.4

3.9406

Cytochrome c oxidase

6

8

16

75

50

3.8664

Oxidoreductase

48

149

207

32.2

72

3.7213

Major histocompatibility complex antigen

13

30

54

43.3

55.6

3.1700

Oxidoreductase, acting on the aldehyde or oxo group of donors

7

13

16

53.8

81.2

3.0285

Carrier

40

131

196

30.5

66.8

2.9960

Complement component

8

16

19

50

84.2

2.9770

P-type ATPase

5

9

11

55.6

81.8

2.6467

Hydrolase, acting on acid anhydrides, catalyzing transmembrane movement of substances

15

42

67

35.7

62.7

2.5199

Nucleobase, nucleoside, nucleotide kinase

7

16

19

43.8

84.2

2.3531

Phosphotransferase, phosphate group as acceptor

5

10

13

50

76.9

2.3520

Glutathione transferase

5

10

13

50

76.9

2.3520

P-P-bond-hydrolysis-driven transporter

17

52

78

32.7

66.7

2.2609

ATP-binding cassette (ABC) transporter

11

30

50

36.7

60

2.2573

Potassium channel

15

45

56

33.3

80.4

2.2093

Carbon-carbon lyase

5

11

18

45.5

61.1

2.0910

  1. All terms with a z score of 2 and at least 5, but less than 100 genes meeting the criterion are shown.
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