Table 3

Over-represented known CREs in N-bicluster 9.

Cis Regulatory Element

% Present in Whole Genome

% Present in N-bicluster 9

P-value


BoxII

49.32%

66.67%

6.90E-05

RAV1A

84.00%

94.44%

1.94E-04

Wbox

80.83%

92.06%

3.40E-04

MYB2CONSENSUSAT

63.96%

78.57%

3.43E-04

RY_repeat

5.36%

13.49%

4.09E-04

ebox

86.24%

95.24%

5.87E-04

DPBF1&2_binding_site_motif

64.32%

77.78%

9.66E-04

ARF

45.03%

59.52%

0.001096

AtMYC2_BS_in_RD22

44.10%

57.94%

0.001509

MYB4

72.72%

84.13%

0.001727

Bellringer/replumless/pennywise BS1 IN AG

42.04%

55.56%

0.001932

SV40

25.69%

38.10%

0.001954

ATB2/AtbZIP53/AtbZIP44/GBF5BS in ProDH

48.52%

61.90%

0.002188

CCA1

34.48%

47.62%

0.002400

ABRE like

26.46%

38.10%

0.004204

AtMYB2 BS in RD22

16.57%

26.19%

0.005280

T box

58.94%

70.63%

0.006024

LFY

62.88%

73.81%

0.007078


Results of a promoter sequence analysis of genes from N-bicluster 9 with the Fisher Exact Test used to determine CRE frequency over-representation in N-bicluster 9. Over-representation of CREs was determined by comparing the frequency of these sites in N-bicluster 9 genes to the frequency in the whole genome as a background. Significance was determined using a 5% FDR cut-off. Indicated in this table is the percentage of genes from the whole genome and N-bicluster 9 that contain these elements and the respective p-values for over-representation. *P-values 0.01–0.05; **P-values 0.001–0.01; ***P-values < 0.001.

Nero et al. BMC Systems Biology 2009 3:59   doi:10.1186/1752-0509-3-59

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