Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

Table 3 Over-representation of four cell cycle related motifs.

Motif	Ace2		Fkh2		Mbp1		Mcm1		Ndd1		Swi4		Swi5
	B+/C+	B+/C-	B+/C+	B+/C-	B+/C+	B+/C-	B+/C+	B+/C-	B+/C+	B+/C-	B+/C+	B+/C-	B+/C+	B+/C-
ACGCGT (MCB)					38.4	8.3					8.2	0.0
CGCGAAA (SCB)					7.0	1.3					19.1	2.8
AACCAGC (Swi5p)	5.1	0.6											2.6	0.8
GTAAACA (SFF)			12.9	1.8			3.1	1.4	8.3	0.6	3.5	0.1

The binomial distribution was used to score motif enrichment in the B+/C+ and B+/C- gene sets for seven cell cycle related transcription factors. The value of -log₁₀(P) is shown only for those combinations of motifs and factors where the motif was significantly overrepresented among the genes bound by the factor. In most cases, the motif is not over-represented in the B+/C- gene group, and in all cases, the over-representation among B+/C- genes is far less significant than among B+/C+ genes.