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

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

Phase Pair_ID1
(p-value)
Genes (1st) Genes (2nd) 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
  1. 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.
  2. 2CorrGenes indicates correlated genes of a module pairs that are regulated in the corresponding phase.
  3. 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 (1st)) and in the second module (Genes (2nd)) 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.