Information content of the database

Short description of the computation of nucleotide frequency matrices for various promoter elements

To get unrelated set of promoters, a pairwise comparison of a region [-50:+1] of 586 plant promoters (including 305 entries from the first release of DB) has been performed and one of the couple of promoters showing more than 90% homology has been excluded from the initial collection. As a result, 10 promoters were excluded from the initial set of the collected promoter sequences.

In simple implementation of Expectation Maximization (EM) algorithm we considered the sequence of motif X=(x₁,x₂,...,x_l) , where l is the motif length. If Pⁱ (x_j) is the empiric frequency of the nucleotide x_j in position i (computed on previous iteration), then the weight of this motif is computed as

W(X) = log ∏ Pⁱ(x_j)/0.25

Using the EM procedure for 10 iterations the initial collection of 576 unrelated promoters was divided into the 2 classes: 345TATA and 231 TATA-less unrelated promoters. In calculations of TATA matrices the allowed variation of a distance between the right boundary of the TATA-core box and the TSS was 18-40 bp and only TATAWAWA-core was used for calculating the weight. As an initial TATA-box matrix, the TATA-matrix computed for 171 plant promoters from the first release of PlantProm DB (http://mendel.cs. rhul.ac.uk/) was used.

For computation of the CCAAT-box matrix we considered the possible distance between the right boundary of CCAAT-core and the TSS within 50-100 bp. As an initial CCAAT-box matrix, the CCAAT-matrix computed for 131 plant promoters from the first release of PlantProm DB (http://mendel.cs. rhul.ac.uk/) was used; in accordance with the available literature data, CCAAT boxes were identified on both DNA strands.

The TSS-motif matrix of 5 bp in length has been computed, where the 3^rd nucleotide was the annotated (anTSS). No strong consensus was revealed. When the EM approach was used to analyze all possible pentanucleotides with an assumed TSS (asTSS) location in the range [anTSS-2:anTSS+2], it was observed that the composition of asTSS-motifs is different in dicot and monocot plants, as well as for TATA and TATA-less promoters.

To search for statistically significant motifs of 1577 known plant regulatory elements, nsite program (http://linux1.softberry. com/berry.phtml) has been applied.