Predicting Gene Regulatory Elements in Silico on a Genomic Scale

Table 2.

Matches to TRANSFAC Binding Sites for the 50 Best Patterns Found for Each 100-bp Upstream Region

−100 −150 −200 −250 −300 −350 −400
Y$ARS1_03 .
Y$ARSH4_02 .       + +  
Y$CAR1_01 +
Y$CAR2_01             +
Y$CDC2_01 . .
Y$CDC9_01     + +      
Y$CEN12_01 + + +
Y$CEN6_01         + + +
Y$CENIV_01 + + +
Y$CFES_01             .
Y$CHA1_04 .
Y$CSVIII_02             +
Y$CTA1_01 + + +
YSCYC1_12   . + + . .  
Y$CYC1_14 + +
Y$DDR2_02           .  
Y$G3PDH_01 . . + +
Y$GAL1_03             +
Y$GAL1_04 . + + . .
Y$GAL1_06             +
Y$GAL1_14 . + + . . +
Y$GAL2_03       + + . +
Y$HO_06 + +
Y$HO_07             .
Y$ICL1_01 +
Y$MAL61_02     .        
Y$MES1_01 + + + +
Y$PDC1_02             .
Y$PGK_01 .
Y$PHO8_02   . + + . .  
Y$POX1_01 . . . .
Y$RAP_01     + + +   +
Y$RP51A_01 +
Y$RPL16A_01           + +
Y$RRNA_01 + + + + +
Y$RRNA_02     + +      
Y$STE6_02 +
Y$SUC2_02       .      
Y$TEF2_01 + +
Y$TOP2_01             +
Y$TRP1_01 + + + +
Y$TRP5_01     + +      
Y$X40_01 + + + +
Y$Y30_01     . + +    

  • For each 100-bp region starting at the seven different positions upstream from ORFs, the 50 highest scoring nontrivial patterns were matched (in substring sense) against the yeast transcription factor binding sites as given in the TRANSFAC (Wingender et al. 1996) database. The first column gives the binding site identifier in TRANSFAC that is matched by one of the best patterns from any of these sets.

  • (+) At least one of the respective patterns matches exactly the corresponding TRANSFAC site.

  • (.) A pattern matches only the reverse-complement of the TRANSFAC site.

This Article

  1. Genome Res. 8: 1202-1215

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