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Table 3 Validation of miRNAs identified by parameterized miRDeep.

From: Characterization of statistical features for plant microRNA prediction

miRNA Family miRNA name Confirmation by RACE Seedling RPM If identified by parameterized miRDeep Reads aligned Star (count)
miR156 zma-MIR156d   14111.2 5932 1
miR156 zma-MIR156l   12645.91 1659 1
miR160 zma-MIR160b 292.65 miRNA overlapping with CDS   
miR162 zma-MIR162 2.74 poor abundance of reads   
miR166 zma-MIR166d   314.6 328 1
miR166 zma-MIR166k 6.52 miRNA homologous to CDS   
miR166 zma-MIR166m 49.75 miRNA homologous to CDS   
miR167 zma-MIR167b 2860.25 17402 1
miR167 zma-MIR167c 2872.95 72684 0
miR168 zma-MIR168a   10364.43 32179 1
miR169 zma-MIR169f   1234.4 3371 0
miR171 zma-MIR171f 15483.87 78 1
miR171 zma-MIR171m   4.12 508 1
miR172 zma-MIR172b   134.49 81 1
miR390 zma-MIR390b   2220.41 6504 1
miR394 zma-MIR394a 4.46 MiRNA overlapping with CDS   
miR396 zma-MIR396f   849.46 2503 1
miR396 zma-MIR396g   43.23 miRNA homologous to CDS   
miR397 zma-MIR397b   556.13 1628 1
miR399 zma-MIR399h   43.23 129 1
miR399 zma-MIR399i   90.57 272 0
miR529 zma-MIR529   359.2 1050 1
miR827 zma-MIR827   711.89 miRNA overlapping with CDS   
Unclassified ?   -   334 0
  1. The candidates were compared against a recently discovered set of miRNAs, from chromosome 5 of maize, expressed in seedlings [14]. The data in third and fourth columns are from [14], while those in last two columns are from current study. The cases missed out by parameterized miRDeep appeared mainly due to a filter which discarded reads mapped to coding sequences (CDS). Even chance homology of a miRNA, either complete or at least in mature/star region, to any CDS can result into the miRNA being unidentified. RPM: Reads Per Million.