Table 2 Phase-specific TF and motif combinations

From: Identifying combinatorial regulation of transcription factors and binding motifs

Phase	Motif combinations*	Over-represented TFs^†				Component motifs^‡	^§ChIP TFs
G1	ACGCGT (-49)	Mbp1	Swi6			ACGCGT	Mbp1	Swi6
	AAACGCG (-35)	Mbp1	Swi4	Swi6		AAACGCG	Mbp1	Swi4	Swi6
	ACGCGA and CGCGAA (-29)	Mbp1	Stb1	Swi4		ACGCGA	Mbp1	Stb1	Swi4
						CGCGAA			Swi4	Swi6^¶
S	CGCGAA[A] and TAAACAA (-09)	Fkh2	Hir1^¶	Swi4	Swi6	CGCGAA			Swi4	Swi6
						CGCGAAA			Swi4
						TAAACAA	Fkh2
S/G2	ATAAACAA (-06)	Fkh2				ATAAACAA	Fkh2
G2/M	GTAAACA and TTAGGAA (-09)	Mcm1	Fkh1	Fkh2	Ndd1	GTAAACA		Fkh1	Fkh2	Ndd1
						TTAGGAA	Mcm1
M/G1	TTAGGAAA (-07)	Mcm1				TTAGGAAA	Mcm1
	TGAAACA[A] and CCAGCA (-09)	Swi5	Dig1	Ste12		TGAAACA		Dig1	Ste12
						TGAAACAA			Ste12
						CCAGCA	Swi5
	AAACGC and ATAATTA (-05)	Mcm1	Swi4^¶			AAACGC		Stb1^¶
						ATAATTA	Mcm1

*Over-represented motif combinations for each cell-cycle phase. Numbers in parentheses represent the exponential part of the p-value for the over-representation. ^†Over-represented TFs in the promoters with a motif combination. ^‡Motifs constituting the corresponding motif combination. ^§ChIP TFs, in the targets of which the 'component motif' to the left is over-represented. ^¶TFs were derived only in either over-represented TFs or ChIP TFs but not in both (as described in Materials and methods).

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