Table 1 List of the identified time-delayed gene regulations for yeast cell cycling. In the bold style are the rules extracted from confident trees and in the regular style are the rules extracted from putative trees.

One-unit time

Two-unit time

Three-unit time

Four-unit time

Five-unit time

CLN1

G1

+SWI5(t) => -CLN1(t+1)

-SWI5(t) => +CLN1(t+1)

-SWI5(t) => +CLN1(t+1)

-SWI5(t) => +CLN1(t+1)

CLN2

G1

+CLB1( t ) => -CLN2( t +1)

-SIC1(t-1) => -CLN2(t+1)

-SIC1(t-1) => -CLN2(t+1)

-SIC1(t-1) => -CLN2(t+1)

-SIC1(t-1) => -CLN2(t+1)

CLN3

M

+CDC53(t) => -CLN3(t+1)

CLB1

M

+CLB6( t ) => -CLB1( t +1)

+CLB6(t) => -CLB1(t+1)

+CLB6( t ) => -CLB1( t +1)

-CLB5(t-4) => -CLB1(t+1)

CLB2

M

+CLB6( t ) => -CLB2( t +1)

+CLB6( t ) => -CLB2( t +1)

+CLB6(t) => -CLB2(t+1)

-CLB5(t-4) => -CLB2(t+1)

CLB4

G2

-CLN1(t) => -CLB4(t+1)

-CLN1(t) => -CLB4(t+1)

-CLB4(t-4) => +CLB4(t+1)

CLB5

G1

CLB6

G1

-SWI5(t) => +CLB6(t+1)

+CLN3(t-3) => +CLB6(t+1)

-CDC20(t-4) => -CLB6(t+1)

MCM1

SIC1

M/G1

+CLN3(t) => +SIC1(t+1)

+CLB2(t-1) => +SIC1(t+1)

-CLN2(t-2) => +SIC1(t+1)

+CLB1( t -3) => +SIC1( t +1)

SWI6

-SKP1(t)-CLN2(t) => -SWI6(t+1)

CDC28

-MBP1(t) => +CDC28(t+1)

-CLB6(t-4) => +CDC28(t+1)

CDC53

MBP1

+MCM1(t-1) => -MBP1(t+1)

-SKP1(t-3) => +MBP1(t+1)

CDC34

-CDC34(t-2) => +CDC34(t+1)

-CDC34(t-4) => +CDC34(t+1)

SWI5

M

+CLB1( t ) => +SWI5( t +1)

-SIC1(t-1) => +SWI5(t+1)

-SIC1(t-1) => +SWI5(t+1)

-SIC1(t-1) => +SWI5(t+1)

-SIC1(t-1) => +SWI5(t+1)

SKP1

-SWI6(t-1) => -SKP1(t+1)

+MBP1(t-2) => +SKP1(t+1)

SWI4

M/G1

+CDC28(t) => +SWI4(t+1)

+CLB2(t-2) => +SWI4(t+1)

+CLB2( t -2) => +SWI4( t +1)

-CLB5(t-4) => +SWI4(t+1)

CDC20

M

-CLB1(t) => -CDC20(t+1)

+CLB1( t -1) => +CDC20( t +1)

+CLB1(t-1) => +CDC20(t+1)

-SWI6(t-3) => -CDC20(t+1)

-SWI6(t-3) => -CDC20(t+1)

HCT1