Table II: Known Cell Cycle Regulated Genes

Gene Symbol	Accession	Phase	Published Reference	Assigned Phase
E2F5	NM_001951	G1	(Sardet et al., 1995;Grosheva et al., 2001)	G2/M
CCNE1	M74093	G1/S	(Lew et al., 1991)	G1/S
CCNE2	NM_004702	G1/S	(Zariwala et al., 1998)	G1/S
CDC25A	NM_001789	G1/S	(Jinno et al., 1994)	G1/S
CDC45L	NM_003504	G1/S	(Saha et al., 1998)	S phase
CDC6	NM_001254	G1/S	(Leone et al., 1998;Yan et al., 1998)	G1/S
CDKN1A, p21	NM_000389	G1/S	(Hiyama et al., 1998)	ND
CDKN3	NM_005192	G1/S	(Gyuris et al., 1993)	M/G1
E2F1	NM_005225	G1/S	(Leone et al., 1998)	G1/S
MCM2	NM_004526	G1/S	(Leone et al., 1998)	G1/S
MCM6	NM_005915	G1/S	(Leone et al., 1998)	G1/S
NPAT	NM_002519	G1/S	(Ma et al., 2000;Zhao et al., 2000)	G1/S
PCNA	NM_002592	G1/S	(Morris and Mathews, 1989)	G1/S
SLBP	NM_006527	G1/S	(Whitfield et al., 2000)	G1/S
BRCA1	NM_007295	S phase	(Rajan et al., 1996)	S phase
BRCA2	NM_000059	S phase	(Rajan et al., 1996;Vaughn et al., 1996)	ND
CCNG2	NM_004354	S phase	(Horne et al., 1996)	ND
CDKN2C	NM_001262	S phase	(Okuda et al., 1995)	G2
DHFR	NM_000791	S phase	(Slansky and Farnham, 1996)	S phase
Histone H1	multiple genes	S phase	(Plumb et al., 1983;Heintz et al., 1983;Harris et al., 1991)	S phase*
Histone H2A	multiple genes	S phase	(Plumb et al., 1983;Heintz et al., 1983;Harris et al., 1991)	S phase*
Histone H2B	multiple genes	S phase	(Plumb et al., 1983;Heintz et al., 1983;Harris et al., 1991)	S phase*
Histone H3	multiple genes	S phase	(Plumb et al., 1983;Heintz et al., 1983;Harris et al., 1991)	ND
Histone H4	multiple genes	S phase	(Plumb et al., 1983;Heintz et al., 1983;Harris et al., 1991)	S phase*
MSH2	NM_000251	S phase	(Marra et al., 1996)	G1/S
NASP	NM_002482	S phase	(Richardson et al., 2000)	G1/S
RRM1	NM_001033	S phase	(Bjorklund et al., 1990)	S phase
RRM2	NM_001034	S phase	(Bjorklund et al., 1990)	S phase
TYMS	NM_001071	S phase	(Kaczmarek, 1986)	S phase
CCNA2	NM_001237	G2	(Pines and Hunter, 1990)	G2
CCNF	NM_001761	G2	(Bai et al., 1994)	G2
CENPF	NM_016343	G2	(Liao et al., 1995)	G2/M
TOP2A	NM_001067	G2	(Goswami et al., 1996)	G2
BIRC5	NM_001168	G2/M	(Li and Altieri, 1999)	G2/M
BUB1	NM_004336	G2/M	(Ouyang et al., 1998)	G2/M
BUB1B	NM_001211	G2/M	(Davenport et al., 1999)	G2/M
CCNB1	NM_031966	G2/M	(Pines and Hunter, 1989)	G2/M
CCNB2	NM_004701	G2/M	(Jackman et al., 1995)	G2/M
CDC2	NM_001786	G2/M	(Dalton, 1992;Zwicker et al., 1995)	G2
CDC20	NM_001255	G2/M	(Weinstein et al., 1994;Weinstein, 1997)	G2/M
CDC25B	NM_021874	G2/M	(Jinno et al., 1994)	G2/M
CDC25C	NM_001790	G2/M	(Zwicker et al., 1995;Lucibello et al., 1995)	G2
CDKN2D, p19	NM_001800	G2/M	(Hirai et al., 1995)	G2/M
CENPA	NM_001809	G2/M	(Shelby et al., 1997)	G2/M
CKS1	BC001425	G2/M	(Richardson et al., 1990)	G2
CKS2	NM_001827	G2/M	(Richardson et al., 1990)	G2/M
PLK	NM_005030	G2/M	(Holtrich et al., 1994;Lee et al., 1995)	G2/M
STK15	NM_003600	G2/M	(Shindo et al., 1998)	G2/M
STK6	NM_003158	G2/M	(Kimura et al., 1997)	NM
RACGAP1	NM_013277	G2/M	(Hirose et al., 2001)	NM
RAB6KIFL	NM_005733	G2/M	(Fontijn et al.	NM

A list of genes was compiled from the literature that had been shown to be cell cycle regulated by traditional methods in cells synchronized independent of serum stimulation. In each case we have listed the primary reference describing the cell cycle regulation of the gene and the predicted cell cycle phase. The cell cycle phase assigned in our study is shown on the right. ND = not detected as cell cycle regulated. NM = not measured on our microarrays. [*] The histone genes were inappropriately assigned to G1/S because they are not polyadenylated and hence behaved sporadically in all experiments except the mitotic selection experiments where total RNA was labeled. Due to extensive literature on the cell cycle regulation of the histone genes and their S phase expression in the mitotic shake-off experiment, the phase was reassigned manually to S phase.