Skip to main content

Table 3 Distribution of differentially expressed (DE) bins among different genomic annotations

From: Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

 

3 hours

6 hours

12 hours

24 hours

48 hours

 

Down-regulated*

Up-regulated*

Down-regulated*

Up-regulated*

Down-regulated*

Up-regulated*

Down-regulated*

Up-regulated*

Down-regulated*

Up-regulated*

Total number of DE bins

8,316

17,348

4,107

6,746

5,276

5,264

6,714

5,464

6,217

3,939

Exonic bins

392

2,053

249

356

299

434

334

258

203

269

Bins that overlap both exons and introns

648

2,597

409

699

492

704

566

617

429

386

Bins that overlap Ensembl exons

127

297

79

92

79

110

101

104

72

58

Bins that overlap exons of Ensembl retained introns

27

78

29

26

24

20

31

32

25

25

Bins that overlap both Ensembl exons and exons of Ensembl retained introns

3

9

1

1

0

2

5

2

0

1

Intronic bins

6,530

10,274

3,041

5,063

4,062

3,515

5,359

3,995

5,070

2,953

Bins that overlap EST (both exons and introns)

75

223

41

65

57

71

50

53

65

46

Bins that overlap EST (exons only)

25

115

23

34

29

46

19

33

21

16

Bins that overlap EST (introns only)

248

527

73

123

86

96

95

99

91

56

Intergenic bins

241

1,175

162

287

148

266

154

271

241

129

Total number of DE bins

100.00 %

100.00 %

100.00 %

100.00 %

100.00 %

100.00 %

100.00 %

100.00 %

100.00 %

100.00 %

Exonic bins

4.71 %

11.83 %

6.06 %

5.28 %

5.67 %

8.24 %

4.97 %

4.72 %

3.27 %

6.83 %

Bins that overlap both exons and introns

7.79 %

14.97 %

9.96 %

10.36 %

9.33 %

13.37 %

8.43 %

11.29 %

6.90 %

9.80 %

Bins that overlap Ensembl exons

1.53 %

1.71 %

1.92 %

1.36 %

1.50 %

2.09 %

1.50 %

1.90 %

1.16 %

1.47 %

Bins that overlap exons of Ensembl retained introns

0.32 %

0.45 %

0.71 %

0.39 %

0.45 %

0.38 %

0.46 %

0.59 %

0.40 %

0.63 %

Bins that overlap both Ensembl exons and exons of Ensembl retained introns

0.04 %

0.05 %

0.02 %

0.01 %

0.00 %

0.04 %

0.07 %

0.04 %

0.00 %

0.03 %

Intronic bins

78.52 %

59.22 %

74.04 %

75.05 %

76.99 %

66.77 %

79.82 %

73.11 %

81.55 %

74.97 %

Bins that overlap EST (both exons and introns)

0.90 %

1.29 %

1.00 %

0.96 %

1.08 %

1.35 %

0.74 %

0.97 %

1.05 %

1.17 %

Bins that overlap EST (exons only)

0.30 %

0.66 %

0.56 %

0.50 %

0.55 %

0.87 %

0.28 %

0.60 %

0.34 %

0.41 %

Bins that overlap EST (introns only)

2.98 %

3.04 %

1.78 %

1.82 %

1.63 %

1.82 %

1.41 %

1.81 %

1.46 %

1.42 %

Intergenic bins

2.90 %

6.77 %

3.94 %

4.25 %

2.81 %

5.05 %

2.29 %

4.96 %

3.88 %

3.27 %

  1. *Relative to the control time point.