The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle

Table 2 Summary of targets controlled by SBF

Ranking	Systematic name	Standard name	Cell cycle peak^a	TF binding^b	Motifs CRCGAA^c	Previous classifications^d	Functional class^e
1	YER001W	MNN1	29	[16-18]	1 (1)	[22,23,36-38]	CW Gly
2	YNL300W	TOS6	30	[15-18]	4	[22,23,35-38]	Unknown
3	YKR013W	PRY2	25	[16-18]	4	[22,23,35,36,38]	Unknown
4	YOL007C	CSI2	24	[15]	4	[22,36]	CW Gly
5	YPL163C	SVS1	28	[15-18]	3 (1)	[22,23,35-38]	Others
6	YPL256C	CLN2	23	[15]	2 (2)	[23,35,36]	DNA RRR/BP
7	YDR297W	SUR2	30	[15]	1	[23]	Others
8	YMR307W	GAS1	36	[15-18]	2 (1)	[22,23,36-38]	CW Gly
9	YDR507C	GIN4	21	[15-18]	1	[23,37,38]	BP
10	YLR183C	TOS4	23	[15]	2 (1)	[22,36]	Others
16	YOL019W		22	[15,17]	1	[36-38]	Unknown
17	YGR140W	CBF2	34	[15]	1 (2)		Cell cycle
18	YNL031C	HHT2	37	[15]	2	[36]	DNA CM
32	YJL173C	RFA3	31		1 (1)		DNA RRR
39	YMR144W		33	[16-18]	1	[35-38]	Unknown
49	YMR179W	SPT21	14	[15-18]	1	[35-38]	Others
51	YPL267W	ACM1	16	[17,18]	1	[35-38]	Unknown
54	YLR121C	YPS3	17	[15]	2	[36]	Others
57	YNL278W	CAF120	nd	[15]	2		Others
61	YHR154W	RTT107	24		1	[36]	DNA RRR
63	YMR304C-A		nd	[16-18]	0		Unknown
65	YHR173C		36		1		Unknown
67	YBL009W	ALK2	36		2		Others
69	YJL080C	SCP160	33		2		Cell cycle
70	YKR090W	PXL1	27		1		BP
71	YGL093W	SPC105	34		1		Cytoskeleton
72	YKL113C	RAD27	20		1	[36]	DNA RRR
73	YBR088C	POL30	20		1	[36]	DNA RRR
76	YGL225W	VRG4	38		2 (1)		CW Gly
77	YDR113C	PDS1	33		0		Cell cycle
79	YLR383W	SMC6	24		1		DNA RRR
81	YGL012W	ERG4	42	[15]	1		Others
84	YPL032C	SVL3	40		1		BP
85	YHR050W	SMF2	nd		1 (1)		Others
86	YKL049C	CSE4	40		1		Cell cycle
87	YBR252W	DUT1	40		1		Others
88	YOR099W	KTR1	34		1 (1)		CW Gly
89	YLL021W	SPA2	31		0 (1)		BP
91	YNL102W	POL1	20		0 (1)	[36]	DNA RRR
92	YJR144W	MGM101	nd		3 (1)		DNA RRR
93	YLR045C	STU2	42		3 (1)	[36]	SPB
94	YAL007C	ERP2	37		1		Others

^aPercent value of the whole duration of the cell cycle taken from [20, 45]. ^bReferences for publications where Swi4 binding was detected. ^cNumber of motifs in the first 400 bp upstream of the TSS (motifs beyond the first 400 bp upstream). ^dReferences for publications where the gene was predicted as target of SBF. ^eCW Gly, cell wall/glycosylation; DNA RRR, DNA replication, recombination and repair; BP, budding/polarity; SPB, spindle pole body; DNA CM, DNA conformation modification. The top ten predicted targets and all those specific (not detected in [22] or [23]) to our classification are shown. The full list is available in Additional file 3. ND, not determined.

ISSN: 1474-760X