Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes

BMC Genomics

Table 1 Top 30 discovered motifs in the promoter regions as ranked by MCS scores

ID	Top Motifs	Genome wide statistics for the aligned region				Functional category enrichment*
		N	k	C.R.	MCS	Most enriched functional category	Genes in functional category	Motif genes in Fun- Group	Enrichment Score
M1	CCCCnC	4734	1462	0.30	93.5	Nucleolus 1	128	75	11.9
M2	CACGTG	623	315	0.50	66.4	Ribosome 2	88	47	24.3
M3	CGTCAY	1970	468	0.23	41.6	Ribosome 2	88	53	5.0
M4	CGCGnC	2195	461	0.21	40.6	Nucleus 2	341	173	9.6
M5	CGCCnC	3007	525	0.17	37.2	-	-	-	-
M6	CCCCnG	2985	509	0.17	36.0	-	-	-	-
M7	CCnCCA	5444	767	0.14	35.4	Nucleus 2	341	178	7.9
M8	CTCCnC	4829	673	0.13	35.2	Peroxisome 2	32	24	5.4
M9	CnCCGMC	1857	357	0.19	33.8	Nucleolus 1	128	43	12.2
M10	CnCnCCC	4201	565	0.13	31.8	Nucleus 3	159	110	6.2
M11	CCAATnA	1105	212	0.19	30.6	-	-	-	-
M12	GCnnCGC	2624	385	0.14	29.3	Cytoskeleton 1	22	15	5.3
M13	ACGYSAC	797	173	0.21	27.9	Nucleus 2	341	150	6.7
M14	CCSGCC	1520	258	0.16	26.5	-	-	-	-
M15	CnGCnCC	3170	421	0.13	26.0	-	-	-	-
M16	CnTCnCC	5870	636	0.10	26.0	-	-	-	-
M17	ACCCCG	761	152	0.19	25.9	-	-	-	-
M18	CGGnCCG	369	93	0.25	25.2	-	-	-	-
M19	AAAAA	6137	668	0.10	24.5	Nucleolus 1	128	113	19.0
M20	CCnCnTC	5505	545	0.09	24.4	-	-	-	-
M21	AAAWTTY	853	169	0.19	23.7	Nucleolus 1	128	101	31.4
M22	TGCCCC	777	139	0.17	22.9	Nucleus 2	341	98	5.4
M23	GnGGCT	2449	321	0.13	21.5	-	-	-	-
M24	GCGCnC	1673	239	0.14	21.2	Nucleus 2	341	196	6.4
M25	TCCCnC	4141	432	0.10	20.8	-	-	-	-
M26	YGATAAG	393	85	0.21	20.2	Nucleolus 1	128	38	10.9
M27	CGACnnC	3725	399	0.10	19.9	-	-	-	-
M28	CCGCnGn	1874	245	0.13	19.7	-	-	-	-
M29	CCTCGGY	381	80	0.20	18.9	Peroxisome 2	32	22	13.5
M30	AnnCCAC	3708	373	0.10	18.6	-	-	-	-

Each motif shown here is the representative motif (i.e. the one with highest MCS score) from each cluster. N and k respectively represent the number of total occurrences in F.g. and the number of occurrences conserved in all four Fusarium genomes. C.R. is the conservation rate of the motif (= k/N) and MCS is the motif conservation score. * The promoter enrichment statistics is for the motif with the highest enrichment score (10^th column) within each cluster shown in the 1^st column. The names of the functional categories are derived from the GO annotation of F. g. The number associated with each category represents the cluster as identified by the k-means clustering on the expression data within each category. Enrichment score is in the unit of -log₁₀(p-value).

ISSN: 1471-2164