MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences

BMC Systems Biology

Table 2 Description of the used 33 datasets

TF	L_seq(bp)	Res	L_bs(min, max, round(avg))	N _seq	N _bs
data group 1 (dg₁): 8 real datasets [32]
CREB	200	H	(05, 30, 12)	17	19
SRF	200	H	(09, 22, 12)	20	35
TBP	200	H	(05, 24, 07)	95	95
MEF2	200	H	(07, 15, 10)	17	17
MYOD	200	H	(06, 06, 06)	17	21
ERE	200	M	(13, 13, 13)	25	25
E2F	200	M	(11, 11, 11)	25	27
CRP	105	E	(22, 22, 22)	18	24
data group 2 (dg₂): 20 artificial datasets [10]
dm01g	1500	D	(13, 28, 20)	04	07
dm04m	2000	D	(10, 26, 15)	04	09
hm02r	1000	H	(10, 36, 23)	09	11
hm03r	1500	H	(14, 46, 27)	10	15
hm06g	500	H	(06, 14, 08)	09	09
hm08m	500	H	(05, 34, 15)	15	13
hm09g	1500	H	(07, 26, 16)	10	10
hm10m	500	H	(07, 09, 08)	06	11
hm11g	1000	H	(06, 42, 14)	08	19
hm16g	3000	H	(09, 54, 23)	07	07
hm17g	500	H	(10, 18, 15)	11	10
hm20r	2000	H	(06, 71, 17)	35	76
hm21g	1000	H	(10, 23, 13)	05	07
hm24m	500	H	(08, 18, 12)	08	08
hm26m	1000	H	(11, 36, 25)	09	10
mus02r	1000	M	(10, 33, 19)	09	12
mus10g	1000	M	(05, 28, 15)	13	15
mus11m	500	M	(06, 27, 15)	12	15
yst08r	1000	M	(12, 49, 21)	11	14
yst09g	1000	Y	(09, 19, 17)	16	13
data group 3 (dg₃): 5 real datasets [33]
CREB	500	H	(05, 30, 12)	17	19
SRF	500	H	(09, 22, 12)	20	36
TBP	500	H	(05, 24, 07)	95	95
MEF2	500	H	(07, 15, 10)	17	17
MYOD	500	H	(06, 06, 06)	17	21

Notations: L_seq denotes the average length of the sequences in base pair count (bp), Res is the resource: (D, H, M, Y, E) refer to (drosophila melanogaster, (human, mouse, rat), saccharomyces cerevisiae, e.coli) respectively, L_bs denotes the length of the binding sites in bp, N_seq is the number of the sequences in the dataset and N_bs is the number of the binding sites in the dataset.

ISSN: 1752-0509