Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

BMC Genomics

Table 1 List of 25 overrepresented motifs identified in this study

Motif family	Motif number	Consensus motif pattern	Algorithms that identified the motifs			No. of clusters whose upstream sequences showed significant overrepresentation
		5′ -> 3′	MEME	AlignACE	FIRE
AP2_1-like	Motif 1	BGCATGCAH	+	+	+	33
	Motif 7	ACATGY	-	-	+	6
	Motif 8	HTGCACH	-	-	+	10
	Motif 11	MAMTGCA	-	-	+	4
	Motif 23	DRMTTSCATB	-	-	+	2
G-box-like	Motif 2	DTGTGGGG	+	+	+	38
	Motif 6	KKGRGGGGRR	+	+	-	16
E2F-like	Motif 3	DTTGSCGCCH	+	+	+	114
	Motif 4	TTTGGCGGGAAV	+	+	-	47
GAGA-like	Motif 5	GDGRRRRARARRRARA	+	+	-	12
	Motif 13	WATTGCA	-	-	+	6
CAAT-box-like	Motif 16	TTTTGCM	-	-	+	7
	Motif 20	BTAKTGCD	-	-	+	8
	Motif 10	RMGACG	-	-	+	1
Unknown set 1	Motif 12	GAGWCA	-	-	+	5
	Motif 15	GAYCTMD	-	-	+	9
	Motif 17	VYGTCBC	-	-	+	1
	Motif 18	WTAGACR	-	-	+	1
	Motif 19	HTAGVTCW	-	-	+	1
	Motif 9	YTTACAT	-	-	+	12
Unknown set 2	Motif 24	KATYTRCAH	-	-	+	3
Other unknown	Motif 14	MAACTA	-	-	+	122
	Motif 21	VRTRAGGAD	-	-	+	3
	Motif 22	HTKWYGAC	-	-	+	5
	Motif 25	WMTAANGA	-	-	+	12

IUPAC codes are used to represent each motif. The algorithm(s) that identified each motif are indicated, as well as the number of clusters containing the overrepresented upstream motif.

ISSN: 1471-2164