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.

Enright et al. Genome Biology 2003 5:R1   doi:10.1186/gb-2003-5-1-r1

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