Table 3

Discovered cis-regulatory clusters for Arabidopsis

d-clust

d-count

related 6-mers

Functional Cluster Name

f-count

P-val


Fig. 6a

95

AATCGC, ATCGCC, CCGACG, CCGATT, CCTCTC, CGATTT, CGCCGA, CTCCGA, CTCTCC, GACTGT, GCCGAC, TCCGAT, TCGCCG, TCTCCG

cysteine-type peptidase activity

8

4.60E-11


Fig. 6b

50

ACACGT, ACGTGT, CACGTG, CGTGTC

response to water deprivation

11

1.50E-11

response to abscisic acid stimulus

12

7.90E-11

PP2C SIG

8

9.80E-11

Protein phosphatase 2C

8

1.20E-10


Fig. 6c

61

CATGCA

nutrient reservoir activity

12

1.80E-18

Seed storage protein

7

6.50E-16


Fig. 6d

66

GGCCCA

cytosolic ribosome

64

1.90E-103

cytosolic part

61

3.10E-99

ribosomal protein

65

3.00E-121

structural constituent of ribosome

65

8.10E-104


Fig. 6e

47

CAACGG

cell cycle

11

7.60E-13

cell division

10

2.00E-12


Fig. 6f

17

GCACGT

plant-type cell wall organization

8

9.80E-14

Extensin-like region

6

7.00E-13

structural constituent of cell wall

6

4.40E-11


'd-clust' is the identifier for the discovered clusters; 'd-count' is the number of genes in the discovered cluster; 'f-count' is the number of genes in the functional clusters, which was discovered by previous well-organized experiments; 'P-value' is measured by Fisher's exact test p-value, which measures the enrichment level of the functions within the discovered cis-regulatory cluster relative to the genome.

Gao et al. BMC Genomics 2013 14(Suppl 1):S4   doi:10.1186/1471-2164-14-S1-S4

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