Supplement 1 | Supplement 2 | Supplement 3    
 
  Supplement 3  
 Regulations identified in 90 genes of the yeast cell cycle.
 Red: certain gene regulation
 Blue: possible gene regulation
 Black: regulation with no supporting evidence

+CLN1(T) -> -SWI5(T+4)
+CLN1(T) -> -MBP1(T+3)
+CLN1(T) -> -CLN3(T+3)
+CLN1(T) -> -ORC2(T+5)
+CLN1(T) -> -LTE1(T+1)
+CLN1(T) -> -MPS1(T+4)
+CLN1(T) -> -BUB3(T+4)
+CLN1(T) -> +APC9(T+4)
+CLN1(T) -> +APC11(T+5)
-CLN1(T) -> -CLB4(T+1)
-CLN1(T+1) -> -CLB4(T+2)
-CLN2(T+2)->+SIC1(T+5)
+CLB6(T) -> -MEC3(T+1)
+CLB6(T) ->-CLB2(T+1)
+CLB6(T+1) ->-CLB1(T+2)
+CLB6(T+1) ->-CLB2(T+2)
+CLB6(T+2) ->-CLB1(T+3)
+CLB6(T+2) ->-CLB2(T+3)
+CLB5(T) -> +CDH1(T+5)
+CLB5(T) -> +MET30(T+1)
+CLB5(T) -> -MCM6(T+2)
+CLB5(T) -> +ORC6(T+3)
+CLB5(T) -> -RFC3(T+5)
+CLB5(T) -> -CDC15(T+3)
+CLB5(T) -> +APC1(T+5)
-SWI5(T) -> +CDC28(T+2)
-SWI5(T) -> +MET30(T+3)
-SWI5(T) -> +CDC45(T+2)
-SWI5(T) -> -MCM6(T+4)
-SWI5(T) -> +ORC6(T+5)
-SWI5(T) -> -ORC2(T+1)
-SWI5(T) -> +RAD53(T+2)
-SWI5(T) -> -CDC15(T+5)
-SWI5(T) -> +BUB1(T+2)
-SWI5(T) -> +SMC1(T+2)
-SWI5(T) -> +SMC3(T+2)
-SWI5(T) -> +APC11(T+1)
+SWI5(T) ->-CLN1(T+1)
-SWI5(T) -> +CLB6(T+1)
+SWI5(T+1)->-CLN1(T+2)
+SWI5(T+3)->-CLN1(T+4)
-CLB1(T) -> +SWI4(T+3)
-CLB1(T) -> +POL1(T+1)
-CLB1(T) -> -ORC4(T+1)
-CLB1(T) -> -MEC3(T+3)
-CLB1(T) -> +BUB2(T+1)
+CLB1(T) ->-CLN2(T+1)
+CLB1(T)-> +SWI5(T+1)
-CLB1(T) ->-CDC20(T+1)
+CLB1(T+1)-> +CDC20(T+3)
+CLB1(T+2)-> +CDC20(T+4)
-CDC20(T) -> -CDC34(T+2)
-CDC20(T) -> -CDC46(T+2)
-CDC20(T) -> +RFC1(T+4)
-CDC20(T) -> -RFC4(T+2)
-CDC20(T) -> +TEM1(T+5)
-CDC20(T) -> -DBF2(T+1)
-CDC20(T) -> +MOB1(T+5)
-CDC20(T) -> -CDC16(T+1)
-MCM1(T) -> -MBP1(T+3)
-MCM1(T) -> -CLN3(T+3)
-MCM1(T) -> -ORC2(T+5)
-MCM1(T) -> -LTE1(T+1)
-MCM1(T) -> -MPS1(T+4)
-MCM1(T) -> -BUB3(T+4)
-MCM1(T) -> +APC9(T+4)
-MCM1(T) -> +APC11(T+5)
+MCM(T+1)-> -MBP1(T+2)
+MCM(T+2)-> -MBP1(T+4)
-SWI6(T) -> +BCK2(T+3)
-SWI6(T) -> +CDC54(T+3)
-SWI6(T) -> +ORC3(T+3)
-SWI6(T) -> -ORC1(T+2)
-SWI6(T) -> -RFC2(T+2)
-SWI6(T) -> +RAD24(T+3)
-SWI6(T) -> +MEC1(T+3)
-SWI6(T) -> -CDC5(T+4)
-SWI6(T) -> -DBF20(T+3)
-SWI6(T) -> +MAD2(T+5)
-SWI6(T) -> -SMC4(T+4)
-SWI6(T) -> -CDC26(T+5)
-SWI6(T) -> +CDC27(T+3)
-SWI6(T+1)->-SKP1(T+2)
-SWI6(T+3) ->-CDC20(T+6)
+CDC28(T) -> +CDH1(T+5)
+CDC28(T) -> +MET30(T+1)
+CDC28(T) -> -MCM6(T+2)
+CDC28(T) -> +ORC6(T+3)
+CDC28(T) -> -RFC3(T+5)
+CDC28(T) -> -CDC15(T+3)
+CDC28(T) -> +APC1(T+5)
+CDC28(T)->+SWI4(T+1)
+CDC53(T) -> -MBP1(T+4)
+CDC53(T) -> -CLN3(T+4)
+CDC53(T) -> +CDC4(T+1)
+CDC53(T) -> -LTE1(T+2)
+CDC53(T) -> -MPS1(T+5)
+CDC53(T) -> -BUB3(T+5)
+CDC53(T) -> +APC9(T+5)
+CDC53(T) -> +CDC23(T+1)
+CDC53(T) -> +APC4(T+1)
+CDC53(T) ->-CLN3(T+1)
-MBP1(T) -> +MET30(T+4)
-MBP1(T) -> +CDC45(T+3)
-MBP1(T) -> -MCM6(T+5)
-MBP1(T) -> -ORC2(T+2)
-MBP1(T) -> +RAD53(T+3)
-MBP1(T) -> -MPS1(T+1)
-MBP1(T) -> -BUB3(T+1)
-MBP1(T) -> +BUB1(T+3)
-MBP1(T) -> +SMC1(T+3)
-MBP1(T) -> +SMC3(T+3)
-MBP1(T) -> +APC9(T+1)
-MBP1(T) -> +APC11(T+2)
-MBP1(T)-> +CDC28(T+1)
+MBP1(T+2)-> +SKP1(T+5)
-CDC34(T) -> -SWI6(T+4)
-CDC34(T) -> -GRR1(T+4)
-CDC34(T) -> +RFC1(T+2)
-CDC34(T) -> -RAD17(T+4)
-CDC34(T) -> +TEM1(T+3)
-CDC34(T) -> +MOB1(T+3)
-CDC34(T+2) -> +CDC34(T+5)
-SKP1(T) -> -CLN3(T+5)
-SKP1(T) -> +CDC4(T+2)
-SKP1(T) -> -POL2(T+1)
-SKP1(T) -> -SRL2(T+1)
-SKP1(T) -> -LTE1(T+3)
-SKP1(T) -> +APC2(T+1)
-SKP1(T) -> +CDC23(T+2)
-SKP1(T) -> +APC4(T+2)
-SKP1(T) ->-SWI4(T+1)
-SKP1(T+3)->-MBP1(T+4)
-CLN3(T) -> +MET30(T+4)
-CLN3(T) -> +CDC45(T+3)
-CLN3(T) -> -MCM6(T+5)
-CLN3(T) -> -ORC2(T+2)
-CLN3(T) -> +RAD53(T+3)
-CLN3(T) -> -MPS1(T+1)
-CLN3(T) -> -BUB3(T+1)
-CLN3(T) -> +BUB1(T+3)
-CLN3(T) -> +SMC1(T+3)
-CLN3(T) -> +SMC3(T+3)
-CLN3(T) -> +APC9(T+1)
-CLN3(T) -> +APC11(T+2)
+CLN3(T) -> +SIC1(T+1)
+CLN3(T)->+CLB6(T+3)
-SWI6(T) -> +BCK2(T+3)
-SWI6(T) -> +CDC54(T+3)
-SWI6(T) -> +ORC3(T+3)
-SWI6(T) -> -ORC1(T+2)
-SWI6(T) -> -RFC2(T+2)
-SWI6(T) -> +RAD24(T+3)
-SWI6(T) -> +MEC1(T+3)
-SWI6(T) -> -CDC5(T+4)
-SWI6(T) -> -DBF20(T+3)
-SWI6(T) -> +MAD2(T+5)


-SWI6(T) -> -SMC4(T+4)
-SWI6(T) -> -CDC26(T+5)
-SWI6(T) -> +CDC27(T+3)
+BCK2(T) -> -ORC5(T+5)
+BCK2(T) -> -CDC5(T+1)
+BCK2(T) -> +MAD2(T+2)
+BCK2(T) -> +MAD1(T+3)
+BCK2(T) -> -SMC4(T+1)
+BCK2(T) -> -CDC26(T+2)
+CDH1(T) -> -PCL1(T+1)
+CDH1(T) -> -DPB11(T+2)
+CDH1(T) -> -MAD3(T+2)
+CDH1(T) -> -ESP1(T+2)
+CDH1(T) -> -DOC1(T+1)
+CLB2(T+1)-> +SIC1(T+3)
+CLB2(T+2)-> +SWI4(T+5)
+CLB2(T+3)->+SWI4(T+6)
-CLB2(T) -> +POL1(T+1)
-CLB2(T) -> -ORC4(T+1)
-CLB2(T) -> -MEC3(T+3)
-CLB2(T) -> +BUB2(T+1)
+MET30(T) -> -PCL1(T+5)
+MET30(T) -> -MCM6(T+1)
+MET30(T) -> +ORC6(T+2)
+MET30(T) -> -RFC3(T+4)
+MET30(T) -> -CDC15(T+2)
+MET30(T) -> -DOC1(T+5)
+MET30(T) -> +APC1(T+4)
-CDC34(T) -> -GRR1(T+4)
-CDC34(T) -> +RFC1(T+2)
-CDC34(T) -> -RAD17(T+4)
-CDC34(T) -> +TEM1(T+3)
-CDC34(T) -> +MOB1(T+3)
-GRR1(T) -> +CDC54(T+3)
-GRR1(T) -> +ORC3(T+3)
-GRR1(T) -> -ORC1(T+2)
-GRR1(T) -> -RFC2(T+2)
-GRR1(T) -> +RAD24(T+3)
-GRR1(T) -> +MEC1(T+3)
-GRR1(T) -> -CDC5(T+4)
-GRR1(T) -> -DBF20(T+3)
-GRR1(T) -> +MAD2(T+5)
-GRR1(T) -> -SMC4(T+4)
-GRR1(T) -> -CDC26(T+5)
-GRR1(T) -> +CDC27(T+3)
+PHO85(T) -> -SLC1(T+1)
+PHO85(T) -> +PCL2(T+1)
+PHO85(T) -> -MCM3(T+2)
+PHO85(T) -> +CDC7(T+2)
+PHO85(T) -> -MCM7(T+2)
+PHO85(T) -> -CDC46(T+4)
+PHO85(T) -> +RFC5(T+2)
+PHO85(T) -> -RFC4(T+4)
+PHO85(T) -> +PDS1(T+2)
+PHO85(T) -> +DUN1(T+2)
+PHO85(T) -> -DBF2(T+3)
+PHO85(T) -> -CDC16(T+3)
-SLC1(T) -> -MCM3(T+1)
-SLC1(T) -> +CDC7(T+1)
-SLC1(T) -> -MCM7(T+1)
-SLC1(T) -> -CDC46(T+3)
-SLC1(T) -> +RFC5(T+1)
-SLC1(T) -> +RFC1(T+5)
-SLC1(T) -> -RFC4(T+3)
-SLC1(T) -> +PDS1(T+1)
-SLC1(T) -> +DUN1(T+1)
-SLC1(T) -> -DBF2(T+2)
-SLC1(T) -> -CDC16(T+2)
-PCL1(T) -> -DPB11(T+1)
-PCL1(T) -> -MAD3(T+1)
-PCL1(T) -> -ESP1(T+1)
+PCL2(T) -> -MCM3(T+1)
+PCL2(T) -> +CDC7(T+1)
+PCL2(T) -> -MCM7(T+1)
+PCL2(T) -> -CDC46(T+3)
+PCL2(T) -> +RFC5(T+1)
+PCL2(T) -> +RFC1(T+5)
+PCL2(T) -> -RFC4(T+3)
+PCL2(T) -> +PDS1(T+1)
+PCL2(T) -> +DUN1(T+1)
+PCL2(T) -> -DBF2(T+2)
+PCL2(T) -> -CDC16(T+2)
+CDC4(T) -> -ORC2(T+5)
+CDC4(T) -> -LTE1(T+1)
+CDC4(T) -> -MPS1(T+4)
+CDC4(T) -> -BUB3(T+4)
+CDC4(T) -> +APC9(T+4)
+CDC4(T) -> +APC11(T+5)
-MCM3(T) -> -CDC46(T+2)
-MCM3(T) -> +RFC1(T+4)
-MCM3(T) -> -RFC4(T+2)
-MCM3(T) -> +TEM1(T+5)
-MCM3(T) -> -DBF2(T+1)
-MCM3(T) -> +MOB1(T+5)
-MCM3(T) -> -CDC16(T+1)
+CDC54(T) -> -ORC5(T+5)
+CDC54(T) -> -CDC5(T+1)
+CDC54(T) -> +MAD2(T+2)
+CDC54(T) -> +MAD1(T+3)
+CDC54(T) -> -SMC4(T+1)
+CDC54(T) -> -CDC26(T+2)
+CDC6(T) -> +CDC7(T+2)
+CDC6(T) -> -MCM7(T+2)
+CDC6(T) -> -CDC46(T+4)
+CDC6(T) -> +RFC5(T+2)
+CDC6(T) -> -RFC4(T+4)
+CDC6(T) -> +PDS1(T+2)
+CDC6(T) -> +DUN1(T+2)
+CDC6(T) -> -DBF2(T+3)
+CDC6(T) -> -CDC16(T+3)
-DBF4(T) -> +CDC7(T+2)
-DBF4(T) -> -MCM7(T+2)
-DBF4(T) -> -CDC46(T+4)
-DBF4(T) -> +RFC5(T+2)
-DBF4(T) -> -RFC4(T+4)
-DBF4(T) -> +PDS1(T+2)
-DBF4(T) -> +DUN1(T+2)
-DBF4(T) -> -DBF2(T+3)
-DBF4(T) -> -CDC16(T+3)
+POL1(T) -> -MEC3(T+2)
+CDC7(T) -> -CDC46(T+2)
+CDC7(T) -> +RFC1(T+4)
+CDC7(T) -> -RFC4(T+2)
+CDC7(T) -> +TEM1(T+5)
+CDC7(T) -> -DBF2(T+1)
+CDC7(T) -> +MOB1(T+5)
+CDC7(T) -> -CDC16(T+1)
-MCM7(T) -> -CDC46(T+2)
-MCM7(T) -> +RFC1(T+4)
-MCM7(T) -> -RFC4(T+2)
-MCM7(T) -> +TEM1(T+5)
-MCM7(T) -> -DBF2(T+1)
-MCM7(T) -> +MOB1(T+5)
-MCM7(T) -> -CDC16(T+1)
-CDC46(T) -> +RFC1(T+2)
-CDC46(T) -> -RAD17(T+4)
-CDC46(T) -> +TEM1(T+3)
-CDC46(T) -> +MOB1(T+3)
+CDC45(T) -> -MCM6(T+2)
+CDC45(T) -> +ORC6(T+3)
+CDC45(T) -> -RFC3(T+5)
+CDC45(T) -> -CDC15(T+3)
+CDC45(T) -> +APC1(T+5)
-MCM6(T) -> +ORC6(T+1)
-MCM6(T) -> -RFC3(T+3)
-MCM6(T) -> -DPB11(T+5)
-MCM6(T) -> -CDC15(T+1)
-MCM6(T) -> -MAD3(T+5)
-MCM6(T) -> -ESP1(T+5)
-MCM6(T) -> -DOC1(T+4)
-MCM6(T) -> +APC1(T+3)
+ORC6(T) -> -RFC3(T+2)
+ORC6(T) -> -DPB11(T+4)
+ORC6(T) -> -MAD3(T+4)
+ORC6(T) -> -ESP1(T+4)
+ORC6(T) -> -DOC1(T+3)
+ORC6(T) -> +APC1(T+2)

+ORC3(T) -> -ORC5(T+5)
+ORC3(T) -> -CDC5(T+1)
+ORC3(T) -> +MAD2(T+2)
+ORC3(T) -> +MAD1(T+3)
+ORC3(T) -> -SMC4(T+1)
+ORC3(T) -> -CDC26(T+2)
-ORC5(T) -> -POL2(T+3)
-ORC5(T) -> -SRL2(T+3)
-ORC5(T) -> -LTE1(T+5)
-ORC5(T) -> +APC5(T+2)
-ORC5(T) -> +APC2(T+3)
-ORC5(T) -> +CDC23(T+4)
-ORC5(T) -> +APC4(T+4)
-ORC1(T) -> +RAD24(T+1)
-ORC1(T) -> +MEC1(T+1)
-ORC1(T) -> -CDC5(T+2)
-ORC1(T) -> -DBF20(T+1)
-ORC1(T) -> +MAD2(T+3)
-ORC1(T) -> +MAD1(T+4)
-ORC1(T) -> -SMC4(T+2)
-ORC1(T) -> -CDC26(T+3)
-ORC1(T) -> +CDC27(T+1)
-ORC2(T) -> +RAD53(T+1)
-ORC2(T) -> -CDC15(T+4)
-ORC2(T) -> +BUB1(T+1)
-ORC2(T) -> +SMC1(T+1)
-ORC2(T) -> +SMC3(T+1)
-ORC4(T) -> -MEC3(T+2)
-RFC2(T) -> +RAD24(T+1)
-RFC2(T) -> +MEC1(T+1)
-RFC2(T) -> -CDC5(T+2)
-RFC2(T) -> -DBF20(T+1)
-RFC2(T) -> +MAD2(T+3)
-RFC2(T) -> +MAD1(T+4)
-RFC2(T) -> -SMC4(T+2)
-RFC2(T) -> -CDC26(T+3)
-RFC2(T) -> +CDC27(T+1)
+RFC5(T) -> +RFC1(T+4)
+RFC5(T) -> -RFC4(T+2)
+RFC5(T) -> +TEM1(T+5)
+RFC5(T) -> -DBF2(T+1)
+RFC5(T) -> +MOB1(T+5)
+RFC5(T) -> -CDC16(T+1)
-RFC3(T) -> -DPB11(T+2)
-RFC3(T) -> -MAD3(T+2)
-RFC3(T) -> -ESP1(T+2)
-RFC3(T) -> -DOC1(T+1)
+RFC1(T) -> +RAD24(T+5)
+RFC1(T) -> +MEC1(T+5)
+RFC1(T) -> -RAD17(T+2)
+RFC1(T) -> +TEM1(T+1)
+RFC1(T) -> -DBF20(T+5)
+RFC1(T) -> +MOB1(T+1)
+RFC1(T) -> +CDC27(T+5)
-RFC4(T) -> -RAD17(T+4)
-RFC4(T) -> +TEM1(T+3)
-RFC4(T) -> +MOB1(T+3)
+RAD24(T) -> -CDC5(T+1)
+RAD24(T) -> +MAD2(T+2)
+RAD24(T) -> +MAD1(T+3)
+RAD24(T) -> -SMC4(T+1)
+RAD24(T) -> -CDC26(T+2)
-POL2(T) -> -LTE1(T+2)
-POL2(T) -> -MPS1(T+5)
-POL2(T) -> -BUB3(T+5)
-POL2(T) -> +APC9(T+5)
-POL2(T) -> +CDC23(T+1)
-POL2(T) -> +APC4(T+1)
+DDC1(T) -> +PDS1(T+3)
+DDC1(T) -> +DUN1(T+3)
+DDC1(T) -> -DBF2(T+4)
+DDC1(T) -> -CDC16(T+4)
-MEC1(T) -> +CBF1(T+1)
-MEC1(T+3) -> +CBF1(T+5)
+MEC1(T) -> -CDC5(T+1)
+MEC1(T) -> +MAD2(T+2)
+MEC1(T) -> +MAD1(T+3)
+MEC1(T) -> -SMC4(T+1)
+MEC1(T) -> -CDC26(T+2)
-RAD17(T) -> -CDC5(T+4)
-RAD17(T) -> -DBF20(T+3)
-RAD17(T) -> +MAD2(T+5)
-RAD17(T) -> -SMC4(T+4)
-RAD17(T) -> -CDC26(T+5)
-RAD17(T) -> +CDC27(T+3)
+RAD53(T) -> -CDC15(T+3)
+RAD53(T) -> +APC1(T+5)
-SRL2(T) -> -LTE1(T+2)
-SRL2(T) -> -MPS1(T+5)
-SRL2(T) -> -BUB3(T+5)
-SRL2(T) -> +APC9(T+5)
-SRL2(T) -> +CDC23(T+1)
-SRL2(T) -> +APC4(T+1)
+PDS1(T) -> +TEM1(T+5)
+PDS1(T) -> -DBF2(T+1)
+PDS1(T) -> +MOB1(T+5)
+PDS1(T) -> -CDC16(T+1)
+DUN1(T) -> +TEM1(T+5)
+DUN1(T) -> -DBF2(T+1)
+DUN1(T) -> +MOB1(T+5)
+DUN1(T) -> -CDC16(T+1)
+TEM1(T) -> -CDC5(T+5)
+TEM1(T) -> -DBF20(T+4)
+TEM1(T) -> -SMC4(T+5)
+TEM1(T) -> +CDC27(T+4)
-LTE1(T) -> -MPS1(T+3)
-LTE1(T) -> -BUB3(T+3)
-LTE1(T) -> +BUB1(T+5)
-LTE1(T) -> +SMC1(T+5)
-LTE1(T) -> +SMC3(T+5)
-LTE1(T) -> +APC9(T+3)
-LTE1(T) -> +APC11(T+4)
+CDC5(T) ->+CDC14(T+1)
+CDC5(T) ->+CDC20(T+1)
+CDC5(T+1) -> + CDC14 (T+2)
+CDC5(T+1) -> +CDC20(T+2)
+CDC5(T+3) -> +CDC20(T+5)
-CDC5(T) -> +MAD2(T+1)
-CDC5(T) -> +MAD1(T+2)
-CDC5(T) -> -CDC26(T+1)
-CDC15(T) -> -MAD3(T+4)
-CDC15(T) -> -ESP1(T+4)
-CDC15(T) -> -DOC1(T+3)
-CDC15(T) -> +APC1(T+2)
-DBF2(T) -> +MOB1(T+4)
-DBF2(T) -> -CDC16(T+0)
-DBF20(T) -> +MAD2(T+2)
-DBF20(T) -> +MAD1(T+3)
-DBF20(T) -> -SMC4(T+1)
-DBF20(T) -> -CDC26(T+2)
+MOB1(T) -> -SMC4(T+5)
+MOB1(T) -> +CDC27(T+4)
+MAD2(T) -> +MAD1(T+1)
+MAD2(T) -> +APC5(T+5)
+MAD1(T) -> +APC5(T+4)
+MAD1(T) -> +APC2(T+5)
-MPS1(T) -> +BUB1(T+2)
-MPS1(T) -> +SMC1(T+2)
-MPS1(T) -> +SMC3(T+2)
-MPS1(T) -> +APC11(T+1)
-BUB3(T) -> +BUB1(T+2)
-BUB3(T) -> +SMC1(T+2)
-BUB3(T) -> +SMC3(T+2)
-BUB3(T) -> +APC11(T+1)
+BUB1(T) -> +APC1(T+5)
-SMC4(T) -> -CDC26(T+1)
+SMC1(T) -> +APC1(T+5)
+SMC3(T) -> +APC1(T+5)
+APC5(T) -> +APC2(T+1)
+APC5(T) -> +CDC23(T+2)
+APC5(T) -> +APC4(T+2)
+APC2(T) -> +APC9(T+5)
+APC2(T) -> +CDC23(T+1)
+APC2(T) -> +APC4(T+1)
+APC9(T) -> +APC11(T+1)
+CDC23(T) -> +APC11(T+5)

 

 
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Biocomputing Lab, School of Computer Science and Engineering, Inha University.
Incheon, 402-751, South Korea. Phone: +82-32-8607388, Fax: +82-32-8634386