Table 2.
Survey by miRDeep2 analysis showing the number of novel and known miRNAs under different score cut-offs ranging from 10 to 1.
| miRDeep2 Score 1 | Novel miRNAs | Known miRNAs | - | ||||
|---|---|---|---|---|---|---|---|
| Predicted 2 | False Positives 3 | True Positives 4 | In Species 5 | In Data 6 | Detected 7 | Signal-to-Noise 8 | |
| 10 | 65 | 3 ± 1 | 62 ± 1 (96% ± 2%) | 411 | 304 | 222 (72%) | 43.7 |
| 9 | 68 | 3 ± 1 | 65 ± 1 (96% ± 2%) | 411 | 304 | 223 (73%) | 43.5 |
| 8 | 69 | 3 ± 2 | 66 ± 3 (96% ± 2%) | 411 | 304 | 223 (73%) | 42.7 |
| 7 | 73 | 3 ± 2 | 70 ± 2 (96% ± 2%) | 411 | 304 | 223 (73%) | 42 |
| 6 | 78 | 3 ± 2 | 75 ± 3 (96% ± 2%) | 411 | 304 | 223 (73%) | 39.7 |
| 5 | 126 | 6 ± 2 | 120 ± 3 (95% ± 2%) | 411 | 304 | 256 (83%) | 30.7 |
| 4 | 156 | 15 ± 4 | 141 ± 4 (90% ± 3%) | 411 | 304 | 259 (84%) | 17.3 |
| 3 | 170 | 42 ± 6 | 128 ± 5 (75% ± 4%) | 411 | 304 | 261 (85%) | 7.5 |
| 2 | 206 | 57 ± 7 | 149 ± 6 (72% ± 3%) | 411 | 304 | 265 (86%) | 6.2 |
| 1 | 300 | 81 ± 8 | 219 ± 7 (73% ± 3%) | 411 | 304 | 278 (91%) | 5.4 |
1 The miRDeep2 score represents the log-odds probability of a sequence being a genuine miRNA precursor versus the probability that it is a background hairpin, given the evidence from the data; 2 Number of novel miRNA hairpins with a score ≥cut-off; 3 Number of false positive miRNA hairpins predicted at this cut-off, as estimated by the miRDeep2 controls. Mean and standard deviation are estimated from 100 rounds of permuted controls; 4 Number of true positive miRNA hairpins is estimated as t = total novel miRNAs—false positive novel miRNAs. The percentage of the predicted novel miRNAs that are estimated to be true positives is calculated as p = t/total novel miRNAs. The number of false positives is estimated from 100 rounds of permuted controls. In each of the 100 rounds, t and p are calculated, generating means and standard deviations of t and p. The variable p can be used as an estimation of the miRDeep2 positive predictive value at the score cut-off; 5 Number of reference mature miRNAs for the pig species given as input to miRDeep2; 6 Number of reference mature miRNAs that map perfectly to one or more of precursor candidates that have been excised from the genome by miRDeep2; 7 Number of reference mature miRNAs that map perfectly to one or more of predicted miRNA hairpins that have a score equal to or exceeding the cut-off. The percentage of reference mature miRNAs in the data that is detected by miRDeep2 is calculated as s = reference mature miRNAs detected/reference mature miRNAs in the data and can be used as an estimation of miRDeep2 sensitivity at the score cut-off; 8 For the given score cut-off, the signal-to-noise ratio is estimated as r = total miRNA hairpins reported/mean estimated false positive miRNA hairpins over 100 rounds of permuted controls.