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Table 2 TSS prediction results for a stepwise increase of cut-off values

From: GC-compositional strand bias around transcription start sites in plants and fungi

Arabidopsis

Rice

GC-skew cutoff

SN (%)

SP (%)

FPR (%)

φ

SN (%)

SP (%)

FPR (%)

φ

-0.9

95.3

13.6

24.4

0.149

98.7

11.6

6.4

0.068

-0.8

95.3

13.6

24.5

0.149

98.7

11.6

6.4

0.068

-0.7

95.3

13.6

24.5

0.150

98.6

11.7

6.5

0.068

-0.6

95.2

13.7

24.7

0.150

98.6

11.7

6.7

0.069

-0.5

95.2

13.7

25.2

0.153

98.4

11.7

7.2

0.072

-0.4

94.9

13.9

26.5

0.157

98.2

11.8

8.4

0.078

-0.3

94.2

14.3

29.4

0.168

97.8

12.1

11.1

0.092

-0.2

93.0

15.1

34.6

0.187

96.6

12.6

16.4

0.115

-0.1

90.7

16.4

42.3

0.213

94.4

13.6

25.3

0.147

0.0

86.7

18.6

52.6

0.247

90.4

15.4

37.9

0.186

0.1

80.0

21.8

64.2

0.282

83.5

18.2

53.2

0.230

0.2

70.2

26.4

75.6

0.315

74.1

22.7

68.5

0.279

0.3

58.7

32.9

85.0

0.345

62.0

29.4

81.4

0.322

0.4

45.0

40.9

91.9

0.354*

47.3

37.7

90.2

0.340*

0.5

31.6

50.5

96.1

0.343

32.3

46.7

95.4

0.327

0.6

20.6

60.6

98.3

0.312

19.1

55.3

98.1

0.281

0.7

11.1

70.2

99.4

0.251

9.1

60.2

99.2

0.204

0.8

4.6

77.4

99.8

0.171

3.2

59.4

99.7

0.119

0.9

1.1

86.9

100.0

0.089

0.8

56.3

99.9

0.057

  1. Only the TSS of genes in which a TIS was defined within the 1.0-kb downstream region are included. Sequence data from 1.0-kb upstream of the TIS (6,850 sequences for Arabidopsis and 13,111 sequences for rice) were used for the TSS prediction. The asterisks denote maximum φ.
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BMC Genomics

ISSN: 1471-2164

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