Table 2

Frequency of KR motifs in CNEs at different gene loci

GENE

# KR motifs in test set

Length of CNE seq for locus (kb)

#hits per kb

# hits in control set (mean)

standard deviation

z-score

p-value


ZNF503

36

27.781

1.30

3.18

1.76

18.62

0.00E+00

TSHZ3

30

23.323

1.29

3.09

1.77

15.23

0.00E+00

IRX5

27

37.059

0.73

5.39

2.33

9.29

0.00E+00

IRX2

21

23.981

0.88

3.10

1.80

9.95

0.00E+00

TSHZ1

16

10.351

1.55

1.63

1.32

10.93

0.00E+00

PBX3

16

17.886

0.89

1.89

1.35

10.44

0.00E+00

HOXD9

16

17.77

0.90

2.19

1.44

9.59

0.00E+00

NR2F2

16

18.99

0.84

2.52

1.59

8.49

0.00E+00

NR2F1

16

25.655

0.62

3.72

1.84

6.67

2.53E-11

MEIS2

16

24.553

0.65

3.42

1.91

6.59

4.49E-11

ZFHX1B

13

23.275

0.56

3.13

1.72

5.73

9.86E-09

SALL3

12

11.405

1.05

1.43

1.21

8.76

0.00E+00

FOXP1

12

15.857

0.76

1.73

1.24

8.25

2.22E-16

MAF

11

7.334

1.50

1.15

1.10

8.95

0.00E+00

NKX6-1

10

6.853

1.46

0.82

0.92

9.94

0.00E+00


Details are shown for the 15 gene loci from the CONDOR CNE set with the highest number of Pbx-Hox KR motifs in their CNEs, showing enrichment relative to shuffled CNE sets (Methods and Additional File 6). For each gene locus, the number of Pbx-Hox KR motifs in the associated CNEs is given. The number of Pbx-Hox KR motifs per kb of CNE sequence for each locus (column 4) is calculated by dividing the number of Pbx-Hox KR motifs in the CNEs of that locus (column 2) by the total combined length of the CNEs in that locus (column 2). Control sets were generated by zero order Markov shuffling of CNEs at each locus in 1000 randomisations (Methods). Some gene loci also contain other genes besides the one after which they are named, for instance the IRX5 locus contains Irx3, Irx5 and Irx6.

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

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