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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)