Table 1.
Comparison between Mirident and previously published software/algorithms.
Figure 1.
The Mirident pipeline.
Figure 2.
A. Effect of increasing number of ss-motifs on miRNA prediction accurracy. Note: The X-axis is discontinuous above 1500 motifs (dashed line). B. The ROC curve of Mirident (red line) trained with 1300 ss-motifs. The Area Under Curve (AUC) is 0.99. Results for other methods are shown for comparison.
Figure 3.
Sequence-structure motif characteristics.
Light hues (pink, light green) indicates the positive and negative randomly selected sequences (RSS). Darker hues (red, green) indicates the actual ss-motifs derived from the positive (pre-miRNA) and negative (CDS hairpin) training sets. A. Combinations of nucleotide and structural information in the ss-motifs. The figure shows occurrence of structural information relative to positions with specific nucleotide information. “Comb” denotes occurrences of specific nucleotide and structural information combined at the same position (e.g., “AL”, “CD”, etc). “Up neighb” and “Dw neighb” denote occurrences of specific nucleotide notation combined with specific structural notations at the nearest upstream or downstream neighbouring position (e.g., “NLAS” etc, and “ASNL” etc), respectively. B. Distribution of “L”, “R” and “D” denotes “left”, “right” and absence of (notation of) intramolecular interactions, respectively.
Figure 4.
Increased ss-motif similiarity within miRNA families.
The panels show the average number of common ss-motif among members of each miRNA family (arrow), compared to a distribution of average pre-miRNAs (repeated 1000 times). A. The miRNA gene family mir-515 (26 members; 172 common ss-motifs). B. The miRNA gene family mir-154 (17 members; 118 common ss-motifs). C. The miRNA gene family let-7 (8 members; 428 common ss-motifs).
Table 2.
Mirident prediction accuracy on non-human and novel pre-miRNA data sets.
Figure 5.
A. ss-motif NLULNSCS is frequently found at the 5′end of the pre-miRNA sequence. B. ss-motif NDNDNDNSNSNSUSGS is concentrated at position 50 in the loop. C&D. Multiple position of similar ss-motifs along the pre-miRNA left strand of has-miR-1302-4 (C) and has-miR-548i-1 (D). It should be noted that the figure shows ss-motif positions in extended pre-miRNA sequences (see Materials and Methods).