Characterization of statistical features for plant microRNA prediction

BMC Genomics

Table 3 Validation of miRNAs identified by parameterized miRDeep.

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

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.

ISSN: 1471-2164