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Table 6 Human-mouse 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

Transcription regulator activity

34

37.65%

128

83.59%

6.63 × 10-4

Over*

Cell-cell signaling

44

26.00%

141

82.27%

1.27 × 10-3

Over*

Development

55

35.19%

157

81.53%

1.41 × 10-3

Over*

Nucleotide binding

42

23.31%

137

79.56%

1.04 × 10-2

Over

Response to biotic stimulus

81

22.67%

273

79.49%

5.62 × 10-4

Over*

Response to external stimulus

65

23.49%

209

79.43%

2.56 × 10-3

Over

Response to stress

91

23.78%

316

79.11%

3.50 × 10-4

Over*

Physiologic process

154

23.59%

526

78.90%

1.37 × 10-6

Over*

Cell proliferation

53

29.13%

209

78.47%

6.00 × 10-3

Over

Receptor binding

65

24.36%

246

77.24%

9.74 × 10-3

Over

Receptor activity

42

24.55%

114

77.19%

4.29 × 10-2

Over

Mitochondrion organization and biogenesis

100

25.26%

266

77.07%

8.93 × 10-3

Over

Transcription

67

35.72%

223

76.68%

1.82 × 10-2

Over

Extracellular region

56

21.66%

217

76.04%

2.73 × 10-2

Over

Protein binding

142

26.43%

464

75.86%

4.75 × 10-3

Over

Extracellular space

54

23.08%

232

75.86%

2.70 × 10-2

Over

Regulation of biologic process

155

29.96%

562

75.27%

4.97 × 10-3

Over

Cytoplasm

45

22.87%

136

74.26%

7.17 × 10-2

 

Plasma membrane

57

20.12%

143

74.13%

7.10 × 10-2

 

Transcription factor activity

42

36.92%

137

73.72%

7.62 × 10-2

 

Nucleus

92

31.28%

332

73.49%

5.00 × 10-2

 

Cell death

48

21.97%

189

73.02%

6.95 × 10-2

 

Protein metabolism

49

19.65%

147

72.79%

7.83 × 10-2

 

Biologic process

35

21.69%

100

72.00%

9.24 × 10-2

 

Signal transduction

116

23.96%

398

71.86%

5.33 × 10-2

 

Cell cycle

41

28.45%

182

70.88%

6.34 × 10-2

 

Cell

118

21.23%

351

69.23%

1.68 × 10-2

Under

Binding

90

24.17%

297

68.69%

1.58 × 10-2

Under

Transport

39

24.11%

146

67.81%

3.30 × 10-2

Under

Catalytic activity

40

19.68%

99

61.62%

4.63 × 10-3

Under

Transporter activity

35

25.00%

123

60.98%

1.20 × 10-3

Under*

  1. The top 31 Gene Ontology (GO) categories in terms of gene numbers in the dataset are shown. The p values given represent the significance (uncorrected) of the observed percentage of conserved (detected) sites, as determined using the Fisher's exact test. Over/under, specifies over-conservation or under-conservation of the sites of the corresponding GO category (by Fisher's exact test) at the 5% significance level. *Statistical over-representation or under-representation after p value correction (using Bonferroni). TFBS, transcription factor binding site.
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Genome Biology

ISSN: 1474-760X

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