Combined analysis reveals a core set of cycling genes

Table 1 Summary of motif-finding results

Budding yeast phase	Transcription factor	Fission yeast cell cycle genes		Negative control (fission yeast non-cell-cycle genes)		Positive control (conserved budding yeast cell-cycle genes)		Extended positive control (all budding yeast CC genes)
G1/S	Swi4	4	43%	0	0%	4	96%	4	98%
	Swi6	4	97%	0	0%	4	100%	4	83%
	Mbp1	4	59%	0	0%	4	93%	4	91%
G2/M	Fkh1	0	0%	2	22%	1	62%	3	67%
	Fkh2	2	45%	2	24%	1	74%	2	67%
	Ndd1	0	0%	0	0%	4	100%	4	100%
M/G1	Mcm1^a	0	0%	0	0%	3	87%	4	88%
	Ace2	4^b	86%	0	0%	0^b	0%	4	88%
	Swi5	~2^b	100%	0	0%	~2^b	75%	1	0%
	Yox1	0^b	0%	0^b	0%	3^b	86%	3	86%
	Yhp1	0^b	0%	0^b	0%	1^b	0%	~1^b	67%

Motif analysis of the conserved cycling genes in budding and fission yeast. For each set and each factor we list the number of motif finders (up to four) that identified the correct motif. Each motif finder often recovers multiple correct motifs, and each motif is associated with a list of predicted instances in promoter regions. We report the percentage of promoters that contain instances predicted by at least one-third of the correct motifs. The first and third columns are the CCC2 genes in budding and fission yeast, respectively. The second column is non-cycling fission yeast genes with homolog cycling budding yeast genes. See Additional data file 3 for further details. ^aMcm1 regulates genes in G2/M and M/G1. ^bThese datasets contain ten genes or fewer. ~, weak matches to the known motif.

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