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

Table 2 Known regulatory elements obtained when applying FastCompare to C. elegans and C. briggsae

Sequence	Rank	D_ATG	W_ATG	Orientation	U/C	Experiment	TRANSFAC	Comments
TGATAAG	5	746	[0;600]	← (p < 10^-6)	1.67	103(56/47)	GATA-1, GATA-2	Known GATA factor
AATCGAT	6	865.5	[0;1900]	-	1.00	14(2/12)	CDP, Clox	Similar to DRE, embryonic development (p < 10^-8)
TGACTCAT	8	708	-	→ (p < 10^-4)	1.40	-	AP-1, GCN4, NF-E2	Known AP-1 site
GTGTTTGC	9	383.5	[0;800]	-	2.44	-	-	Known forkhead-related activator 4
CACGTGG	16	935	-	-	0.73	12(9/3)	Myc/Max, PHO4, USF	Known Myc-Max site in Drosophila
AAGGTCA	22	882	[0;1400]	-	1.52	35(16/19)	ER, HNF-4	Known HRE
TGACGTC	32	858	[0;1700]	-	0.94	1(1/0)	CREB, ATF	Known CREB site
TGTCATCA	42	879	-	-	0.80	-	Skn-1	Known SKN-1 site
CAGCTGG	56	1093	[100;2000]	-	0.67	5(2/3)	AP-4, HEN-1	Known AP-4 and MyoD/CeMyoD site
AGAGAGA	57	893	-	→ (p < 10^-90)	1.43	4(2/2)	-	Known GAGA-factor site
GTAAACA	79	818	[0;400]	-	2.69	28(28/0)	Freac, SRY	Known DAF-16 site
CCCGCCC	88	535	[0;1400]	-	2.48	1(0/1)	Sp1, GC box	Known Sp1 site
ATCAATCA	100	911	-	-	0.93	1(1/0)	Pbx-1	Known Pbx-1 site
CAGGTGA	111	845	[0;200]	-	2.25	-	Lmo2, RAV1	Known Snail site in Drosophila
TTCGCGC	148	651.5	[0;1200]	-	1.7	16(7/9)	E2F	Known E2F site, embryonic development (p < 10^-6)

For each known regulatory element, we show the best k-mer, its rank within the set of 437 highest scoring k-mers, the median distance to ATG (for occurrences upstream of genes within the conserved set), the optimal window, the orientation bias, the corrected ratio of upstream/coding bias, the total (up-regulated/down-regulated) number of microarray conditions in which the k-mer was found (see Materials and methods), TRANSFAC matches, and the best GO enrichment.

ISSN: 1474-760X