Skip to main content

Table 2 Example of predicting the presence of transcription factor binding sites in the upstream regulatory region of the papillomaviruses.

From: Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

  α β γ   α β γ
  HPV16 HPV18 HPV6 HPV8 HPV4   HPV16 HPV18 HPV6 HPV8 HPV4
AbaA + +   + + HFH-8 + + + + +
AhR/Arnt +   +    HLF +     
AP-1 + + + + + HNF-3beta +   + + +
AREB6 + + + + + lk-1      +
Arnt +   +   + Lmo2 complex   + + + +
Athb-1 +     + Mat1-Mc + + + +  
Bcd   + + + + MATa1     +  
Brc- Z1     +   Max +     
BR-c Z4 + + + +   MCM1 +     
Brn-2 +   + + + MYB.Ph3 +     +
CCAAT box    +    NF-E2     +  
C/EBP   +   +   NF-Y   + + + +
CDP CR3+HD   +   +   Nkx2-5 +   +   
c-Ets-1(p54) + + +   + N-Myc +     
CF2-II + + + + + NRF-2      +
CHOP-C   + + +   oct-1 + + + + +
c-Myb + + + + + OCT-x      +
c-Myc/Max +      PacC    +   +
Croc +    +   PHO4 +   +   +
dl   +    + RAP1   +    
E2 + + + + + RFX1   +    
E2F   +     RORalpha1 +   +   
E47   + + + + S8 + + +   +
E74A      + SBF-1   + + + +
Elf-1 + + + + + Skn-1 + + + + +
Elk-1 +     + Sn   + + +  
ER +     + Sox-5 + + + + +
FOXD3 +   + + + SOX-9 + + + + +
FOXJ2 + + + +   STATx     + +
Freac-2 +   + +   StuAp   + +   
Freac-7 + + + + + Su(H)   +    
GATA-1   + + + + TATA + + +   +
GATA-2   + +   + TCF11     +  
GATA-3   +     TGIF +     +
GATA-x   + + + + USF +   +   
GBP +   +   + VBP    +   
GCN4 +   + + + v-ErbA    +   
Gfi-1 +      v-Maf +     
Hand1/E47     + + v-Myb + + + + +
Hairy    +    XFD-1 +    +  
HAP2/3/4      + XFD-2 +   + +  
HFH-1 +   + +   YY1 +     
HFH-3 + + + + + Zeste     + +
  1. Transcription factor binding sites were predicted with MATCH, using the nucleotide matricial description of each site as compiled in TRANSFAC. The coincidence levels between the binding site sequence and the sequence in the URR were fixed to optimise simultaneously the number of false positives and false negatives. It is obvious that different papillomaviruses contain different transcription factor binding sites in their URR. Some of them are common to all papillomaviruses, such as AP-1, E2, HFH-3 or Oct-1. Other TFBS are type-exclusive, genus-exclusive, or are shared by papillomaviruses that infect the same host. The high dimensionality of these results makes it necessary to analyse them with information reduction techniques, such as principal component analysis or genetic algorithms.