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Table 2 List of the identified time-delayed gene regulations for human Hela 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.

From: Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling

Gene Name

Peak phase

Time Delayed

  

One-unit time

One-unit time

Three-unit time

Four-unit time

Five-unit time

PCNA

G1/S

 

+E2F1(t-1)+CCNA2(t-1)-CDC20(t-1) => +PCNA(t+1)

   

NPAT

G1/S

   

-CDC2( t -1) => +NPAT( t +1)

 

E2F1

G1/S

+BUB1B(t) => -E2F1(t+1)

  

+BUB1B(t) => -E2F1(t+1)

 

CCNE1

G1/S

+CDC2( t )-CDC25B( t ) => +CCNE1( t +1)

+CDC2( t -1)+CDC20( t -1) => +CCNE1( t +1)

+CDC2( t -1)+CDC20( t -1) => +CCNE1( t +1)

+CDC2(t-1)+CDC20(t-1) => +CCNE1(t+1)

-CCNF(t)-CDC20(t-4) => -CCNE1(t+1)

CDC25A

G1/S

-CCNE1(t)-CCNE1(t) +CDC20(t) => -CDC25A(t+1)

  

-CCNE1(t)-BUB1B(t-1) => +CDC25A(t+1)

-CCNE1(t)-STK15(t) => +CDC25A(t+1)

CDKN1A

G1/S

-CDKN1A(t)-DHFR(t) => +CDKN1A(t+1)

-CDKN1A(t)-DHFR(t-1) => +CDKN1A(t+1)

-CDKN1A(t)-BRCA1(t-2) => +CDKN1A(t+1)

-CDKN1A(t)+CDC20(t-3) => +CDKN1A(t+1)

-CDKN1A(t)+CDC20(t-3) => +CDKN1A(t+1)

BRCA1

S

     

DHFR

S

 

+BUB1B( t -1)+CDC25A( t -1) => +DHFR( t +1)

   

TYMS

S

     

CCNF

G2

+CDC2( t ) -BUB1B( t ) => -CCNF( t +1)

+CDC2(t)-STK15(t-1) => -CCNF(t+1)

-CDC2(t)+CDC25C(t) => +CCNF(t+1)

+CDC2( t ) => +CCNF( t +1)

+CDC2( t ) => +CCNF( t +1)

CCNA2

G2

-CDC2(t)+STK15(t) => +CCNA2(t+1)

+CDC2(t)-STK15(t-1) => -CCNA2(t+1)

 

+CDC2(t) => +CCNA2(t+1)

+CDC2( t ) => +CCNA2( t +1)

CDC20

G2/M

-STK15(t)-CKS2(t) => -CDC20(t+1)

-STK15( t )+CDC20( t -1) => +CDC20( t +1)

-STK15( t )+CDC20( t -2) => +CDC20( t +1)

-CKS2(t)-CDC20(t-3) => +CDC20(t+1)

+CCNE1(t)+TYMS(t) => +CDC20(t+1)

STK15

G2/M

-CCNF( t )-CCNE1( t ) => +STK15( t +1)

-CCNF( t )-CCNE1( t ) => +STK15( t +1)

+CDC2( t -1)+CDC20( t -1) => -STK15( t +1)

-CDC2( t -1) => -STK15( t +1)

-CCNF( t ) => -STK15( t +1)

BUB1B

G2/M

  

+CDC2(t-1)+CDC20(t-1) => -BUB1B(t+1)

+CDC2(t-1)+CDC20(t-1) => -BUB1B(t+1)

+CDC2(t-1)+CDC20(t-1) => -BUB1B(t+1)

CKS2

G2/M

-CCNF( t )-PCNA( t ) => +CKS2( t +1)

+CCNA2( t -1)-BRCA1( t -1) => -CKS2( t +1)

+CCNA2( t -1)-BRCA1( t -1) => -CKS2( t +1)

+CCNA2( t -1)+CKS2( t -3) => -CKS2( t +1)

-STK15(t) => -CKS2(t+1)

CDC25C

G2/M

 

+CDC2(t)+TYMS(t)-CDKN1A(t-1) => +CDC25C(t+1)

+CDC2(t)+TYMS(t)-CDKN1A(t-1) => +CDC25C(t+1)

+CDC2( t )+TYMS( t )+PCNA( t -3) => +CDC25C( t +1)

+CDC2( t )+CDC25A( t -4)-CDC20( t -3) => +CDC25C( t +1)

PLK

G2/M

-STK15( t )-CCNF( t ) => -PLK( t +1)

-STK15( t )-CCNF( t ) => -PLK( t +1)

-STK15( t )-CCNF( t ) => -PLK( t +1)

-STK15( t )-CCNF( t ) => -PLK( t +1)

-STK15( t )-CKS2( t -4) => +PLK( t +1)

CCNB1

G2/M

     

CDC25B

G2/M

-CKS2(t)-CDKN1A(t)-BUB1B(t) => -CDC25B(t+1)

-CKS2(t)+PCNA(t-1) => +CDC25B(t+1)

 

-CKS2( t )-CDC20( t -2) => +CDC25B( t +1)

-CKS2(t)-CDC20(t-4) => +CDC25B(t+1)

CDC2

G2/M

-CDC2(t) => -CDC2(t+1)

   

-E2F1(t-4) => -CDC2(t+1)