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Table 3 Gene ontology enrichment for human switch-like genes.

From: Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality

  

Human bimodal genes

Mouse bimodal genes

Gene Ontology

Genes Observed

Genes Expected

Ration of Enrichment

P-values

Genes Observed

Genes Expected

Ration of Enrichment

P-values

CC

Cytoplasm

527

408.92

1.29

0.00E+00

395

335.13

1.18

3.73E-05

 

cytoskeleton

110

57.49

1.91

0.00E+00

68

41.97

1.62

1.91E-05

 

sarcoplasmic reticulum

14

2.40

5.83

5.39E-10

10

2.49

4.02

2.06E-05

 

membrane

680

577.01

1.18

2.03E-08

494

442.64

1.12

9.12E-04

 

striated muscle thick filament

12

2.26

5.31

6.39E-08

7

1.99

3.52

1.25E-03

 

muscle myosin complex

12

2.54

4.72

4.94E-07

0

N/A

N/A

N/A

 

actin cytoskeleton

36

15.68

2.30

6.87E-07

11

8.13

1.35

1.78E-01

 

myosin complex

21

6.92

3.03

9.19E-07

13

5.81

2.24

2.76E-03

 

neuromuscular junction

6

0.85

7.08

7.89E-06

6

2.65

2.26

3.69E-02

 

cell junction

62

37.01

1.68

2.09E-05

55

28.20

1.95

2.64E-07

 

Z disc

9

1.98

4.55

2.24E-05

8

3.48

2.30

1.51E-02

 

synapse

41

22.04

1.86

4.26E-05

41

20.07

2.04

2.33E-06

 

membrane fraction

97

66.25

1.46

5.02E-05

32

27.71

1.15

2.10E-01

 

growth cone

10

2.68

3.73

8.41E-05

9

3.32

2.71

2.72E-03

 

plasma membrane

239

192.10

1.24

9.90E-05

169

143.67

1.18

9.51E-03

 

cell projection

23

11.02

2.09

3.38E-04

19

10.62

1.79

6.35E-03

 

costamere

4

0.57

7.08

3.97E-04

1

0.66

1.51

5.16E-01

 

clathrin coat of trans-Golgi network vesicle

6

1.27

4.72

4.51E-04

0

N/A

N/A

N/A

 

sarcoplasmic reticulum membrane

6

1.27

4.72

4.51E-04

5

1.16

4.31

1.95E-03

 

proteinaceous extracellular matrix

52

33.62

1.55

7.38E-04

60

28.04

2.14

1.47E-09

 

integral to plasma membrane

184

148.88

1.24

9.15E-04

53

47.62

1.11

2.14E-01

 

troponin complex

5

0.99

5.06

9.16E-04

6

1.33

4.52

4.27E-04

 

axon

10

3.81

2.62

2.62E-03

18

7.96

2.26

3.97E-04

 

sarcolemma

6

1.70

3.54

3.39E-03

13

3.82

3.41

1.51E-05

 

basement membrane

12

5.79

2.07

9.14E-03

17

5.81

2.93

1.12E-05

 

collagen

7

2.83

2.48

1.60E-02

14

4.81

2.91

7.34E-05

 

postsynaptic membrane

19

12.71

1.49

4.48E-02

21

10.29

2.04

6.69E-04

 

I band

2

0.42

4.72

5.42E-02

4

0.66

6.03

7.55E-04

 

synaptic vesicle membrane

1

0.28

3.54

2.63E-01

6

1.33

4.52

4.27E-04

 

basal lamina

2

1.13

1.77

3.15E-01

9

2.49

3.62

1.79E-04

BP

muscle contraction

39

12.43

3.14

0.00E+00

10

2.82

3.55

9.66E-05

 

striated muscle contraction

21

4.10

5.13

0.00E+00

11

3.15

3.49

5.21E-05

 

cell adhesion

112

65.68

1.71

3.76E-09

81

44.63

1.81

1.67E-08

 

nervous system development

79

42.38

1.86

1.36E-08

33

22.40

1.47

1.19E-02

 

muscle development

29

10.03

2.89

2.95E-08

14

5.31

2.64

2.72E-04

 

sensory perception of sound

33

15.26

2.16

8.44E-06

5

4.98

1.00

5.72E-01

 

glycolysis

19

7.06

2.69

2.44E-05

15

6.97

2.15

2.11E-03

 

regulation of heart contraction

13

3.96

3.29

4.01E-05

9

3.48

2.58

4.07E-03

 

cytoskeleton organization and biogenesis

24

10.74

2.24

7.75E-05

26

13.11

1.98

2.72E-04

 

antigen processing and presentation of peptide antigen via MHC class I

7

1.41

4.96

8.99E-05

6

2.49

2.41

2.67E-02

 

dephosphorylation

24

10.88

2.21

9.77E-05

11

9.12

1.21

2.98E-01

 

regulation of muscle contraction

8

1.84

4.36

1.03E-04

13

2.82

4.61

8.48E-08

 

regulation of striated muscle contraction

6

1.13

5.31

1.71E-04

2

0.50

4.02

7.34E-02

 

central nervous system development

25

12.01

2.08

1.99E-04

5

4.81

1.04

5.39E-01

 

cell differentiation

72

47.88

1.50

1.99E-04

54

49.44

1.09

2.57E-01

 

multicellular organismal development

136

102.41

1.33

2.26E-04

84

85.11

0.99

5.73E-01

 

regulation of the force of heart contraction

5

0.85

5.90

2.96E-04

4

1.66

2.41

6.86E-02

 

neuromuscular synaptic transmission

5

0.85

5.90

2.96E-04

3

1.16

2.58

9.46E-02

 

neuron migration

12

4.10

2.93

3.05E-04

8

8.63

0.93

6.50E-01

 

neuron differentiation

13

4.66

2.79

3.08E-04

4

5.81

0.69

8.55E-01

 

glycogen metabolic process

12

4.24

2.83

4.44E-04

3

3.32

0.90

6.68E-01

 

protein amino acid dephosphorylation

29

15.54

1.87

5.06E-04

11

11.95

0.92

6.67E-01

 

tricarboxylic acid cycle

10

3.39

2.95

9.10E-04

6

3.65

1.64

1.44E-01

 

very-long-chain fatty acid metabolic process

5

0.99

5.06

9.16E-04

1

0.50

2.01

4.20E-01

 

ion transport

83

62.01

1.34

2.89E-03

67

44.13

1.52

1.88E-04

 

transport

218

188.15

1.16

8.19E-03

188

153.46

1.23

9.54E-04

 

calcium ion transport

20

11.72

1.71

1.03E-02

21

8.96

2.34

7.22E-05

 

synaptic transmission

35

24.01

1.46

1.28E-02

21

7.96

2.64

8.49E-06

MF

actin binding

78

34.32

2.27

0.00E+00

42

27.04

1.55

1.76E-03

 

structural constituent of muscle

28

5.65

4.96

0.00E+00

5

1.49

3.35

8.74E-03

 

structural molecule activity

81

42.52

1.91

3.01E-09

58

34.01

1.71

1.53E-05

 

structural constituent of cytoskeleton

32

12.15

2.63

8.12E-08

22

11.45

1.92

1.26E-03

 

protein binding

777

677.86

1.15

1.68E-07

558

497.39

1.12

1.79E-04

 

calmodulin binding

37

16.95

2.18

1.93E-06

23

13.11

1.75

3.73E-03

 

motor activity

33

14.69

2.25

3.40E-06

28

13.60

2.06

7.77E-05

 

calcium ion binding

145

103.40

1.40

8.50E-06

116

76.98

1.51

1.37E-06

 

GTPase activity

43

24.15

1.78

8.61E-05

22

19.74

1.11

3.24E-01

 

phosphoprotein phosphatase activity

31

15.96

1.94

1.52E-04

10

13.44

0.74

8.85E-01

 

phosphoric monoester hydrolase activity

25

11.87

2.11

1.61E-04

12

10.12

1.19

3.07E-01

 

microfilament motor activity

9

2.40

3.75

1.82E-04

3

1.00

3.01

6.15E-02

 

NAD binding

13

4.52

2.88

2.14E-04

3

4.48

0.67

8.49E-01

 

transferase activity, transferring phosphorus-containing groups

7

1.55

4.51

2.17E-04

6

1.66

3.62

2.36E-03

 

protein tyrosine phosphatase activity

25

12.43

2.01

3.59E-04

14

10.62

1.32

1.65E-01

 

transporter activity

61

40.68

1.50

6.35E-04

41

33.18

1.24

8.24E-02

 

long-chain-fatty-acid-CoA ligase activity

6

1.41

4.25

9.92E-04

3

1.33

2.26

1.33E-01

 

creatine kinase activity

3

0.57

5.31

1.01E-02

4

0.66

6.03

7.55E-04

 

extracellular matrix structural constituent

18

10.88

1.65

1.96E-02

18

6.80

2.65

3.52E-05

 

ion channel activity

48

36.02

1.33

2.15E-02

46

25.38

1.81

2.17E-05

  1. GO category enrichment was computed using the set of human bimodal genes as well as the previously identified bimodal genes in mouse. GO terms enriched with p ≤ 0.001 in both bimodal human genes and the set of bimodal mouse genes are shown in bold. Italicized values do not meet the p ≤ 0.001 significance threshold
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