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Table 7 Human-opossum TFBS conservation dependency on the GO category of the downstream regulated gene

From: Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

GO category

Number of genes

Upstream Coverage

Detectable TFBSs

% TFBS Detected

p value

Over/under

Receptor binding

51

6.49%

180

55.56%

5.80 × 10-6

Over*

Cell-cell signaling

35

6.37%

120

51.67%

3.67 × 10-3

Over

Physiologic process

122

5.63%

415

49.40%

1.51 × 10-6

Over*

Response to external stimulus

54

5.60%

168

48.81%

6.12 × 10-3

Over

Transcription regulator activity

32

10.15%

122

47.54%

2.47 × 10-2

Over

Extracellular space

43

4.08%

175

47.43%

1.23 × 10-2

Over

Response to biotic stimulus

60

5.29%

209

47.37%

7.82 × 10-3

Over

Transcription

61

10.52%

208

45.67%

2.13 × 10-2

Over

Transcription factor activity

40

9.80%

133

45.11%

4.65 × 10-2

Over

Development

47

9.48%

120

45.00%

5.25 × 10-2

 

Signal transduction

86

5.72%

293

44.71%

1.95 × 10-2

Over

Response to stress

74

6.23%

268

44.03%

3.18 × 10-2

Over

Regulation of biologic process

134

8.49%

490

43.06%

2.59 × 10-2

Over

Cell

82

6.11%

241

40.66%

5.96 × 10-2

 

Nucleus

81

10.05%

305

40.66%

5.52 × 10-2

 

Extracellular region

44

6.17%

160

40.63%

6.95 × 10-2

 

Cell proliferation

49

7.63%

196

40.31%

6.26 × 10-2

 

Mitochondrion organization and biogenesis

77

6.90%

213

39.44%

5.29 × 10-2

 

Cytoplasm

34

6.07%

97

39.18%

7.95 × 10-2

 

Cell death

41

6.77%

164

37.80%

4.34 × 10-2

Under

Protein binding

122

7.01%

419

35.80%

4.81 × 10-4

Under*

Cell cycle

39

7.67%

176

35.23%

1.35 × 10-2

Under

Nucleotide binding

32

5.82%

112

31.25%

5.81 × 10-3

Under

Protein complex

28

5.90%

84

29.76%

7.37 × 10-3

Under

DNA binding

27

10.05%

74

29.73%

1.08 × 10-2

Under

Binding

71

6.77%

240

29.58%

5.58 × 10-6

Under*

Receptor activity

31

6.53%

88

29.55%

5.67 × 10-3

Under

Plasma membrane

37

4.78%

91

28.57%

3.00 × 10-3

Under

Protein metabolism

41

6.27%

131

25.95%

3.75 × 10-5

Under*

Transporter activity

31

6.28%

91

23.08%

6.74 × 10-5

Under*

Transport

32

5.53%

102

20.59%

1.85 × 10-6

Under*

  1. See Table 6 footnote for details.