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Table 1 Normalized Experimental Affinity of Cluster-sites

From: The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes

  Number of Half-sites
  2 3 4 5 5.5 6 7 7.5 8 8.5 9 10 11 12
Cluster Site Relative Binding Affinity
DDB2 1   5            
TP53I3   3    6    10   12    16  
Theoretical Affinity Approximations
# of Full-sites with spacers ≤ 14 bp 1 3 5 7 8 9 11 12 13 14 15 17 19 21
# of Full-sites with spacers ≤ 24 bp 1 3 6 9 10.5 12 15 16.5 18 19.5 21 24 27 30
# of Full-sites with any size spacer 1 3 6 10   15 21   28   36 45 55 66
  1. This table contains the normalized experimental affinities of different cluster-sites dependent upon the number of half-sites contained in the RE. These affinity measurements were obtained by mutating or truncating p53 cluster-sites in the genes DDB2, and TP53i3 [20, 21]. These two p53 cluster-sites are chosen because they match the assumption of the theoretical models that no spacer sequences are present between the half-sites. All affinities are normalized by the 2 half-site (full-site) affinity respective of the RE. The theoretical models assume that all the half-sites in each cluster-site are identical, which is not the case for either of the two cluster-sites. Experimental results support a linear affinity growth model based upon the number of full-sites with spacers no longer than 14 bp (in italics).