Table 1.
Validation of prediction method on experimentally verified miRNA targets
| MiRNA | Organism | Target gene (3' UTR) | Number of experimental sites | Number of predicted sites | Rank | Number of predicted sites with conservation | Matches experimental to predicted | Matches experimental to predicted (%) |
| lin-4 | cel/cbr | lin-14 (Abnormal cell-lineage protein 14) | 7 | 1 | 0 | 0 | 0% | |
| lin-4 | cel/cbr | lin-28 | 1 | 1 | 4/1,014 | 1 | 1 | 100% |
| lin-4 | cel/cbr | lin-41a lin41b | 1 | 1 | 5/1,014 | N/A | 1† | 100%† |
| let-7 | cel/cbr | lin-14 (Abnormal cell-lineage protein 14) | 2 | 6 | 9/1,014 | 2 | 2 | 100% |
| let-7 | cel/cbr | lin-28 | 1 | 1 | 12/1,014 | 1 | 1 | 100% |
| let-7 | cel/cbr | lin-41a lin41b | 2 | 6 | 2/1,014 | N/A | 2† | 100%† |
| let-7 | cel/cbr | daf-12 | 3 | 10 | 7/1,014 | 1 | 1 | 33% |
| let-7 | cel/cbr | hbl-1 (hunchback-related protein) | 8 | 14 | 1/1,014 | 8 | 5 | 63% |
| bantam | dme/dps | hid (Head involution defective (wrinkled)) | 2 | 2 | 1/11,318 | 2 | 2 | 100% |
| miR-13 | dme/dps | CG10222 | 1 | 1 | 4/11,318 | 1 | 1 | 100% |
Using intermediate thresholds (S: 80; ΔG: -14 kcal/mol), for each known miRNA and target gene pair (in either C. elegans or D. melanogaster), we list the number of known experimental target sites, the number of sites detected here, both raw and conserved in C. briggsae or D. pseudoobscura; and, the number and percentage of known sites that correspond to computationally detected conserved sites, with larger values indicating more successful (retrospective) prediction († and 'N/A' indicate that no 3' UTR was available to scan against in C. briggsae, hence no conservation analysis was possible, results assume conservation). cel/cbr: C. elegans/C. briggsae; dme/dps: D. melanogaster/D. pseudoobscura.