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Table 1 The co-occurrence in the same promoter of DNA motifs that cluster

From: Comparative genomics of Drosophila and human core promoters

 

Motif

  

DMp1

DMp2

DMp3

DMp4

DMp5

DMv1

DMv2

DMv3

DMv4

DMv5

NDM1

NDM2

NDM3

NDM4

NDM5

 

Ohler no.

  

3

4

 

9

  

8

7

1

6

   

2

5

 

Name

  

TATA

INR

INR1

DPE1

DPE2

     

GAGA

  

DRE

E-box

 

Totals

 

8289

511

1501

113

80

147

311

311

604

649

287

359

424

215

1593

1184

(a)

STATAAA

DMp1

511

 

98

9

2

4

2

8

10

6

4

19

28

9

21

26

 

TCAGTY

DMp2

1501

98

 

12

25

43

15

18

34

17

12

100

108

38

67

112

 

TCATTCG

DMp3

113

9

12

 

0

5

3

2

2

4

1

10

5

5

9

9

 

CGGACGT

DMp4

80

2

25

0

 

1

1

2

4

2

2

10

6

1

6

9

 

KCGGTTSK

DMp5

147

4

43

5

1

 

3

0

2

4

3

14

11

7

4

18

 

CARCCCT

DMv1

311

2

15

3

1

3

 

16

13

18

6

5

7

7

79

46

 

TGGYAACR

DMv2

311

8

18

2

2

0

16

 

8

15

6

4

6

6

59

64

 

CAYCNCTA

DMv3

604

10

34

2

4

2

13

8

 

18

9

1

16

9

282

63

 

GGYCACAC

DMv4

649

6

17

4

2

4

18

15

18

 

64

8

12

12

95

59

 

TGGTATTT

DMv5

287

4

12

1

2

3

6

6

9

64

 

0

5

2

26

38

 

GAGAGCG

NDM1

359

19

100

10

10

14

5

4

1

8

0

 

26

18

6

28

 

CGMYGYCR

NDM2

424

28

108

5

6

11

7

6

16

12

5

26

 

6

33

34

 

GAAAGCT

NDM3

215

9

38

5

1

7

7

6

9

12

2

18

6

 

22

33

 

ATCGATA

NDM4

1593

21

67

9

6

4

79

59

282

95

26

6

33

22

 

265

 

CAGCTSWW

NDM5

1184

26

112

9

9

18

46

64

63

59

38

28

34

33

265

 
 

Unique

 

4156

304

932

58

30

48

146

146

220

366

141

165

195

88

783

534

 

Totals

 

8289

511

1501

113

80

147

311

311

604

649

287

359

424

215

1593

1184

(b)

STATAAA

DMp1

511

4.7

6.5

8.0

2.5

2.7

0.6

2.6

1.7

0.9

1.4

5.3

6.6

4.2

1.3

2.2

 

TCAGTY

DMp2

1501

19.2

13.8

10.6

31.3

29.3

4.8

5.8

5.6

2.6

4.2

27.9

25.5

17.7

4.2

9.5

 

TCATTCG

DMp3

113

1.8

0.8

1.0

0.0

3.4

1.0

0.6

0.3

0.6

0.4

2.8

1.2

2.3

0.6

0.8

 

CGGACGT

DMp4

80

0.4

1.7

0.0

0.7

0.7

0.3

0.6

0.7

0.3

0.7

2.8

1.4

0.5

0.4

0.8

 

KCGGTTSK

DMp5

147

0.8

2.9

4.4

1.3

1.4

1.0

0.0

0.3

0.6

1.1

3.9

2.6

3.3

0.3

1.5

 

CARCCCT

DMv1

311

0.4

1.0

2.7

1.3

2.0

2.9

5.1

2.2

2.8

2.1

1.4

1.7

3.3

5.0

3.9

 

TGGYAACR

DMv2

311

1.6

1.2

1.8

2.5

0.0

5.1

2.9

1.3

2.3

2.1

1.1

1.4

2.8

3.7

5.4

 

CAYCNCTA

DMv3

604

2.0

2.3

1.8

5.0

1.4

4.2

2.6

5.5

2.8

3.1

0.3

3.8

4.2

17.7

5.3

 

GGYCACAC

DMv4

649

1.2

1.1

3.5

2.5

2.7

5.8

4.8

3.0

6.0

22.3

2.2

2.8

5.6

6.0

5.0

 

TGGTATTT

DMv5

287

0.8

0.8

0.9

2.5

2.0

1.9

1.9

1.5

9.9

2.6

0.0

1.2

0.9

1.6

3.2

 

GAGAGCG

NDM1

359

3.7

6.7

8.9

12.5

9.5

1.6

1.3

0.2

1.2

0.0

3.3

6.1

8.4

0.4

2.4

 

CGMYGYCR

NDM2

424

5.5

7.2

4.4

7.5

7.5

2.3

1.9

2.7

1.9

1.7

7.2

3.9

2.8

2.1

2.9

 

GAAAGCT

NDM3

215

1.8

2.5

4.4

1.3

4.8

2.3

1.9

1.5

1.9

0.7

5.0

1.4

2.0

1.4

2.8

 

ATCGATA

NDM4

1593

4.1

4.5

8.0

7.5

2.7

25.4

19.0

46.7

14.6

9.1

1.7

7.8

10.2

14.6

22.4

 

CAGCTSWW

NDM5

1184

5.1

7.5

8.0

11.3

12.2

14.8

20.6

10.4

9.1

13.2

7.8

8.0

15.4

16.6

10.9

 

Unique

  

59.5

62.1

51.3

37.5

32.7

47.0

47.0

36.4

56.4

49.1

46.0

46.0

40.9

49.2

45.1

 

Totals

 

8289

511

1501

113

80

147

311

311

604

649

287

359

424

215

1593

1184

(c)

STATAAA

DMp1

511

 

3.2

0.8

0.3

0.5

4.1

1.1

4.1

7.3

2.4

0.2

1.1

0.1

14.2

5.4

 

TCAGTY

DMp2

1501

3.2

 

0.4

4.1

5.9

6.5

5.1

10.2

22.6

7.0

11.8

10.1

0.9

40.4

5.6

 

TCATTCG

DMp3

113

0.8

0.4

 

0.1

1.4

0.0

0.1

1.0

0.4

0.4

2.1

0.0

0.8

1.3

0.4

 

CGGACGT

DMp4

80

0.3

4.1

0.1

 

0.0

0.2

0.0

0.0

0.6

0.0

3.3

0.7

0.0

1.1

0.0

 

KCGGTTSK

DMp5

147

0.5

5.9

1.4

0.0

 

0.1

1.6

1.7

0.9

0.0

3.2

1.3

1.3

5.5

0.2

 

CARCCCT

DMv1

311

4.1

6.5

0.0

0.2

0.1

 

1.5

0.5

0.0

0.2

1.0

0.8

0.1

6.3

1.5

 

TGGYAACR

DMv2

311

1.1

5.1

0.1

0.0

1.6

1.5

 

1.8

0.3

0.2

1.4

1.1

0.0

1.4

6.3

 

CAYCNCTA

DMv3

604

4.1

10.2

1.0

0.0

1.7

0.5

1.8

 

3.1

1.1

7.4

0.9

0.3

84.2

0.1

 

GGYCACAC

DMv4

649

7.3

22.6

0.4

0.6

0.9

0.0

0.3

3.1

 

19.9

2.9

2.4

0.0

0.0

0.8

 

TGGTATTT

DMv5

287

2.4

7.0

0.4

0.0

0.0

0.2

0.2

1.1

19.9

 

3.9

1.2

0.8

2.2

0.6

 

GAGAGCG

NDM1

359

0.2

11.8

2.1

3.3

3.2

1.0

1.4

7.4

2.9

3.9

 

2.5

3.3

16.8

1.2

 

CGMYGYCR

NDM2

424

1.1

10.1

0.0

0.7

1.3

0.8

1.1

0.9

2.4

1.2

2.5

 

0.3

4.7

1.2

 

GAAAGCT

NDM3

215

0.1

0.9

0.8

0.0

1.3

0.1

0.0

0.3

0.0

0.8

3.3

0.3

 

1.1

1.3

 

ATCGATA

NDM4

1593

14.2

40.4

1.3

1.1

5.5

6.3

1.4

84.2

0.0

2.2

16.8

4.7

1.1

 

13.5

 

CAGCTSWW

NDM5

1184

5.4

5.6

0.4

0.0

0.2

1.5

6.3

0.1

0.8

0.6

1.2

1.2

1.3

13.5

 
  1. The 15 motifs are grouped into three groups, DMp1 to 5, DMv1 to 5, and NDM1 to 5. (a) The number of promoters that contain two motifs, each that occurs in a peak, was determined. To the left are the 15 motifs followed by the number of their occurrences in the peak. (b) The frequency of promoters containing one motif also containing a second motif. DMp1 (TATA) for example, is found in 4.7% of all promoters but occurs in 6.5% of promoters that contain DMp2 (INR). (c) The probability. Throughout all three panels of the table, positive correlations are shown as normal numbers, negative correlations are underlined and if the probability term has a value p ≤ 10-5, one in 100,000, then the numbers are in bold. For example, INR is found in 1,501 promoters, which is 13.8% of all promoters. However, in the 1,593 DRE promoters, the INR only occurs in 4.2% of them. This observed under-representation or negative correlation has a one in 1040 probability occurring by chance.
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Genome Biology

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