Table 1.
The Numbers of Training Sequences for Building Discriminative Models
Table 2.
The Numbers of Pol II Promoter Sequences from Different Species Included in the Training Set for Plant Models
Table 3.
The Numbers of Different class-III Promoters in Pol III Training and Test Sets
Table 4.
Results of 10-Fold Cross-Validations of SVM and Decision-Tree Models
Table 5.
Error Rates of SVM Models on Independent Test Sets
Table 6.
Classification Results of MicroRNA Genes Using the Known Pre-MicroRNAs and Pri-MicroRNA
Figure 1.
The Distribution of the Distances between Putative Promoters and MicroRNA Hairpins
The horizontal axis shows the positions of putative promoters with respect to the corresponding microRNA hairpins and the vertical axis shows the percentage of microRNA genes that have putative promoters at the specified positions.
Table 7.
The Results of Promoter Prediction by CoVote and TSSP on A. thaliana MicroRNA Genes Whose Promoters Were Identified by Xie et al. [22]
Figure 2.
Significant Conserved Motifs Discovered in the Putative Promoters of the Four Species
(A) The number of microRNA genes that contain the corresponding motifs in their upstream.
(B) Expected frequencies of the corresponding motifs.
(C) Z-scores obtained by Monte Carlo Simulations (see the section Motif Analysis).
Figure 3.
The Distributions of CT Repeats
The first group to the left of the figure shows the distributions of CT repeats in the genomes of the four species studied, estimated by a Monte Carlo simulation. The subsequent groups show the distributions of CT repeats in the upstream of microRNA hairpins. The vertical axis is the percentage of microRNA genes and randomly sampled sequences that contain CT repeats (see text).
Table 8.
The Distances between CT Repeats and TSSs in the Promoters of 40 of 52 A. thaliana MicroRNA Genes Analyzed by Xie et al. [22]
Table 9.
Putative CpG Islands in the Upstream Regions of Corresponding Hairpinned pre-MicroRNAs
Figure 4.
Significant Species-Specific Motifs Discovered in the Putative Promoters of MicroRNA Genes in Four Species.
(A–C) The same as in Figure 2.