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

BMC Bioinformatics

Table 1 Normalized Experimental Affinity of Cluster-sites

	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

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).

ISSN: 1471-2105