Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Table 3 Novel predicted regulatory elements obtained when applying FastCompare to C. elegans and C. briggsae

Sequence	Rank	D_ATG	W_ATG	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.

ISSN: 1474-760X