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Table 2 Overrepresented Gene Ontology classes in the gastrocnemius as compared to the quadriceps

From: The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way

GO ID

GO class

N

Raw Score

FDR

GO:0001974

blood vessel remodeling

15

1.99

2.39E-10

GO:0006776

vitamin A metabolic process

15

1.92

9.95E-11

GO:0051705

behavioral interaction between organisms

18

1.63

3.89E-04

GO:0006775

fat-soluble vitamin metabolic process

20

1.57

4.17E-04

GO:0048705

skeletal morphogenesis

17

1.41

8.14E-04

GO:0009855

determination of bilateral symmetry

31

1.30

5.97E-11

GO:0003007

heart morphogenesis

29

1.28

8.53E-11

GO:0014033

neural crest cell differentiation

31

1.28

3.98E-10

GO:0006936

muscle contraction

69

1.19

1.49E-10

GO:0006937

regulation of muscle contraction

25

1.19

7.35E-04

GO:0043010

camera-type eye development

56

1.14

7.02E-11

GO:0007368

determination of left/right symmetry

30

1.14

8.02E-04

GO:0048762

mesenchymal cell differentiation

38

1.13

9.19E-11

GO:0008016

regulation of heart contraction

34

1.13

3.23E-04

GO:0060047

heart contraction

41

1.11

1.09E-10

GO:0007498

mesoderm development

44

1.06

1.33E-10

GO:0001654

eye development

82

1.03

7.46E-11

GO:0048592

eye morphogenesis

37

1.02

6.97E-04

GO:0006766

vitamin metabolic process

56

1.01

6.28E-11

GO:0009952

anterior/posterior pattern formation

86

0.96

4.59E-11

GO:0016055

Wnt receptor signaling pathway

107

0.94

4.98E-11

GO:0042445

hormone metabolic process

71

0.92

1.71E-04

GO:0048771

tissue remodeling

104

0.92

1.71E-10

GO:0006875

cellular metal ion homeostasis

57

0.92

2.99E-04

GO:0048637

skeletal muscle development

61

0.92

7.96E-11

GO:0006959

humoral immune response

52

0.92

7.46E-04

GO:0007519

striated muscle development

103

0.91

1.19E-10

GO:0055065

metal ion homeostasis

58

0.91

1.99E-04

GO:0030324

lung development

59

0.89

4.07E-04

GO:0007178

transmembrane receptor protein serine/threonine kinase signaling pathway

67

0.89

1.93E-04

GO:0006575

amino acid derivative metabolic process

70

0.88

5.69E-11

GO:0030323

respiratory tube development

60

0.88

4.78E-04

GO:0007229

integrin-mediated signaling pathway

74

0.88

2.91E-04

GO:0048469

cell maturation

66

0.87

4.68E-04

GO:0006817

phosphate transport

61

0.86

2.84E-04

GO:0055074

calcium ion homeostasis

53

0.86

7.58E-04

GO:0045786

negative regulation of progression through cell cycle

101

0.85

5.19E-11

GO:0048732

gland development

63

0.85

6.85E-04

GO:0044271

nitrogen compound biosynthetic process

61

0.84

3.98E-04

GO:0030003

cellular cation homeostasis

87

0.84

1.99E-10

GO:0021700

developmental maturation

79

0.84

2.21E-04

GO:0016311

dephosphorylation

105

0.83

5.97E-10

GO:0055080

cation homeostasis

88

0.83

2.13E-04

GO:0055082

cellular chemical homeostasis

90

0.82

5.43E-11

GO:0006470

protein amino acid dephosphorylation

93

0.82

6.63E-11

GO:0050778

positive regulation of immune response

75

0.81

3.32E-04

GO:0051240

positive regulation of multicellular organismal process

94

0.81

1.76E-04

GO:0008015

circulation

84

0.81

5.43E-04

GO:0050776

regulation of immune response

88

0.80

1.87E-04

GO:0002684

positive regulation of immune system process

77

0.80

4.59E-04

GO:0050801

ion homeostasis

103

0.79

2.99E-10

GO:0002682

regulation of immune system process

90

0.79

2.06E-04

GO:0001503

ossification

80

0.79

4.51E-04

GO:0045165

cell fate commitment

94

0.78

4.42E-04

GO:0015674

di-, tri-valent inorganic cation transport

112

0.78

1.19E-09

GO:0031214

biomineral formation

81

0.78

7.21E-04

GO:0046849

bone remodeling

89

0.78

3.81E-04

GO:0008361

regulation of cell size

91

0.77

4.78E-11

GO:0030005

cellular di-, tri-valent inorganic cation homeostasis

81

0.77

7.08E-04

GO:0043062

extracellular structure organization and biogenesis

85

0.77

6.28E-04

GO:0009968

negative regulation of signal transduction

81

0.77

6.74E-04

GO:0040008

regulation of growth

117

0.77

1.81E-04

GO:0006816

calcium ion transport

85

0.75

8.78E-04

GO:0002009

morphogenesis of an epithelium

103

0.73

4.87E-04

GO:0002252

immune effector process

106

0.73

6.40E-04

GO:0043549

regulation of kinase activity

120

0.72

3.14E-04

GO:0045859

regulation of protein kinase activity

115

0.72

3.73E-04

GO:0051338

regulation of transferase activity

121

0.72

3.06E-04

  1. ErmineJ was used to identify significantly overrepresented GO classes in the gastrocnemius as compared with the quadriceps from LFD mice (n = 10). For the concept biological process we selected GO classes with a FDR < 0.001. For this analysis only classes containing 8 through 125 genes were taken into account. N, number of genes in GO class