Table 3

Novel predicted regulatory elements obtained when applying FastCompare to C. elegans and C. briggsae

Sequence

Rank

DATG

WATG

Orientation

U/C

Experiment

Comments


CTGCGTCT

1

635.5

-

→ (p < 10-10)

2.70

-

Unknown site

CGACACTCC

4

234

[0;1500]

-

2.49

-

Unknown site, positive regulation of growth (p < 10-7)

CTCCGCCC

14

440

[0;900]

-

3.51

2(2/0)

Unknown site, similar to Sp1

CGAGACC

20

738

[0;1900]

-

1.34

30(7/23)

Unknown site, embryonic development (p < 10-7)

CGCGACGC

23

457

[0;1900]

-

2.34

-

Unknown site

ATTTCGCAA

29

641

[0;1900]

-

2.50

1(0/1)

Unknown site

CGTAAATC

31

514

[0;600]

-

2.78

-

Unknown site

TTGCGGAC

39

253

[0;1700]

-

1.43

-

Unknown site

ATGATGCAA

44

600

[0;1600]

-

0.88

-

Unknown site

CGCGCTC

46

576

[0;900]

-

2.73

2(0/2)

Unknown site

TGGCGCC

49

770.5

[0;1800]

-

1.01

-

Unknown palindromic site

AACCGGTT

50

651

[0;1900]

-

1.41

-

Unknown palindromic site

TAAAGGCGC

61

524

[0;700]

-

8.67

27(12/15)

Unknown site

CGCGCGC

120

455

[0;600]

-

5.40

11(3/8)

Unknown site

CTAATCC

228

934

-

→ (p < 10-7)

1.20

-

Unknown homeodomain site, similar to Bicoid

TACCGTA

242

975

[0;500]

-

2.23

20(18/2)

Unknown site


k-mers shown here were selected from the list of 437 highest scoring k-mers based on their short median distance to ATG, short optimal window, significant orientation bias, strong over-representation ratio (U/C), presence in upstream regions of over/underexpressed genes in several microarray conditions, palindromicity or resemblance to known sites in other species.

Elemento and Tavazoie Genome Biology 2005 6:R18   doi:10.1186/gb-2005-6-2-r18

Open Data