A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle

Table 2 Phase-related cooperative module pairs (the top three).

Phase	Pair_ID¹ (p-value)	Genes (1^st)	Genes (2^nd)	CorrGenes²
Early G1 (3, 4)	93(30,32) (0.000168)	SWI4, CDC28, BNI1, FUS1	FUS3, STE5, CCD28, CLN2, CLN3	SWI4, FAR1
(5, 6)	50(42,30) (0.00174)	CDC28, CDC34, CDC4, CLN2	CDC28, BNI1, SLT2, PKC1, SWE1	CDC6, FAR1
(7, 8)	37(32,0) (0.0066)	CDC28, CLN2, CLN3, STB1	RAD9, RAD53, SWI6, MRC1, MEC1, CDC45	SWI4
Late G1 (9, 10, 11)	13(0,30) (6.68E-11)	RAD18, RAD6, RAD53, CLB5	SWE1, CDC28, SWI4	HO, CLB6, SWE1
(12, 13)	20(0,15) (0)	RAD53, RAD52,	RAD1, RAD14	CDC9
(14, 15, 16)	15(0,10) (0)	POL30,POL32, RAD9	MSH2, MSH3, MSH6, MLH1, EXO1	POL30, MSH6, MSH2
S (17, 18)	2(3,0) (7.52E-09)	CIN8, KIP3, MAD2	RAD53, DUN1, MEC1, CDH1	CIN8,PDS1
(19, 20)	43(37,17) (4.07E-08)	SPC24,DAM1, CBF2	MTW1, NNF1, NSL1, DSN1, NDC80	MTW1,SPC25,SPC110, CBF2
(21, 22)	34(3,27) (1.71E-06)	BIM1, CIN8, KAR9	BIK1	CIN8, BIM1
G2 (23)	1(1,0) (0.00027)	MOB1, SWI4, SIC1, CDC28	DBF2, LTE1, CLB2, SRS2	MOB1, SRS2, DBF20
(24, 25, 26)	5(39,0) (0.00015)	GCN5, SPT8	RAD51, RAD53, ASF1, RAD6, MEC1	HTZ1
(27, 28)	50(42,30) (0.0029)	CDC34, CDC4, CDC28	SWE1, PKC1	ELM1, CHS2
M (29, 30)	47(30,14) (2.3E-08)	PCL2, PHO85, CDC28	SWI5, ACE2, FKH2, FKH1, NDD1	CLB3, SWI5, ACE2, CDC5, BUD4, CDC28
(31, 32)	92(3,79) (2.95E-08)	BUB3, CLB3, CLB5	SIC1, CLB5, CDC28	CLB3, CLB1, CLB4, CDC20
(33, 34, 35)	93(30,32) (8.91E-05)	SLT2,CDC12, CDC28	CLN1, CLN2, FUS3, CDC28	MSG5, BUD2

¹Pair_ID indicates the unique identifier of each identified module pair; (ID_1, ID_2): indicates the unique identifiers (IDs) of the first and second modules of a module pair, respectively.
²CorrGenes indicates correlated genes of a module pairs that are regulated in the corresponding phase.
To discover cooperative module pairs essential for controlling cell cycle progression, we ranked the 67 phase-related module pairs (complete results in Additional file 8) according to the number of phase-regulated genes correlated with each module pair and then listed the top three module pairs for each phase. The statistical significance of the cooperation of a module pair (p -value) and the ID of a module pair are listed in the second column. To assess the effects and mechanisms of cooperation, a subset of regulated correlated genes for each module pair and genes demonstrated to be associated with these correlated genes are also listed in the table. These genes include genes contained in the first module (Genes (1^st)) and in the second module (Genes (2^nd)) of a module pair. The references for these cooperative interactions are listed in Additional file 1 Table A1. The serial numbers of these references are shown in the first column.

ISSN: 1471-2105