Table 1

Frequency of KR motifs, compared to shuffled versions, in different test sets

Motif

CONDOR CNEs (from [57])

Human:Shark CNEs (from 13]

VISTA EB (all) [43]

VISTA EB set HB/BA/CN+ve (from [43])

VISTA EB set HB +ve (from [43])

Zebrafish CBset all [21]

Zebrafish CB set HB +ve (from [21])


TGATNNATKR

562

666

609

161

131

17

7

TGTANNATKR

171

188

388

65

52

12

3

GTATNNATKR

150

168

279

54

39

9

2

GTTANNATKR

150

178

325

79

65

8

2

TTGANNATKR

200

245

447

80

64

9

1

TTAGNNATKR

167

238

398

74

55

7

0

ATGTNNATKR

259

297

452

86

72

20

1

ATTGNNATKR

233

297

436

74

61

20

2

AGTTNNATKR

215

254

431

85

68

9

0

TAGTNNATKR

147

154

297

54

42

10

4

TATGNNATKR

176

198

365

74

60

10

3

GATTNNATKR

274

315

419

97

74

11

0

TGATNNTAKR

106

143

314

65

50

6

1

TGTANNTAKR

142

151

421

82

60

14

1

GTATNNTAKR

59

73

195

41

34

1

0

GTTANNTAKR

105

108

253

50

33

5

0

TTGANNTAKR

162

205

385

72

62

10

0

TTAGNNTAKR

73

97

235

41

31

0

0

ATGTNNTAKR

103

124

376

64

55

3

0

ATTGNNTAKR

136

158

305

57

42

6

1

AGTTNNTAKR

85

121

320

64

50

5

1

TAGTNNTAKR

66

69

198

37

27

1

0

TATGNNTAKR

84

94

345

80

62

5

1

GATTNNTAKR

144

177

292

58

42

2

0

mean

165.38

196.58

353.54

70.58

55.46

8.33

1.25

S.D

102.75

122.06

93.73

24.74

20.92

5.52

1.67

z-score for pbxhox

3.86

3.84

2.72

3.65

3.61

1.57

3.43

p-value

5.68E-05

6.16E-05

3.30E-03

1.00E-04

2.00E-04

N/S

3.00E-04


Enrichment analysis for Pbx-Hox KR motifs, relative to shuffled versions (retaining G+C content for each binding site), within different sets of CNEs. CNEs from the VISTA enhancer browser (EB) and zebrafish cneBrowser (CB) sets have also been grouped according to annotated expression in the hindbrain (HB), branchial arches (BA) or cranial nerves (CN). All sequences are human except the Zebrafish cneBrowser set. N/S = not significant

Parker et al. BMC Genomics 2011 12:637   doi:10.1186/1471-2164-12-637

Open Data