MicroRNA targets in Drosophila

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.

ISSN: 1474-760X