Table 2

Summary of the top de novo miRNA target predictions based on the Argonaute PAR-CLIP data

Cluster

miRbase ID

8-mer

Expression rank

miRNA score

P-value

Number of targets

Cumulative number of targets

1

hsa-mir-16-2

TGCTGCTA

22

17.93

3.0E-20

438

438 (3%)

hsa-mir-15b

TGCTGCTA

53

17.93

3.5E-20

438

438 (3%)

hsa-mir-15a

TGCTGCTA

64

17.93

3.5E-20

438

438 (3%)

hsa-mir-195

TGCTGCTA

NA

17.93

3.5E-20

438

438 (3%)

hsa-mir-16-1

TGCTGCTA

NA

17.93

3.5E-20

438

438 (3%)

hsa-mir-103-2

ATGCTGCT

2

14.41

9.7E-13

620

620 (5%)

hsa-mir-107

ATGCTGCT

39

14.41

9.7E-13

620

620 (5%)

hsa-mir-103-1

ATGCTGCT

NA

14.41

9.7E-13

620

620 (5%)

hsa-mir-424

TGCTGCTG

60

12.92

1.5E-08

632

632 (5%)

hsa-mir-497

TGCTGCTG

133

12.92

1.5E-08

632

632 (5%)

hsa-mir-646

AGCTGCTT

NA

10.5

1.1E-06

708

708 (6%)

hsa-mir-503

CGCTGCTA

97

10.08

1.7E-07

714

714 (6%)

2

hsa-mir-106b

GCACTTTA

5

17.63

8.9E-17

455

1,164 (9%)

hsa-mir-20a

GCACTTTA

9

17.63

8.9E-17

455

1,164 (9%)

hsa-mir-106a

GCACTTTT

121

15.65

1.6E-15

565

1,272 (10%)

hsa-mir-519c

TGCACTTT

NA

14.71

7.6E-21

689

1,395 (11%)

hsa-mir-519c-3p

TGCACTTT

NA

14.71

7.6E-21

689

1,395 (11%)

hsa-mir-519a-2

TGCACTTT

NA

14.71

7.6E-21

689

1,395 (11%)

hsa-mir-519b-3p

TGCACTTT

NA

14.71

7.6E-21

689

1,395 (11%)

hsa-mir-519a-1

TGCACTTT

NA

14.71

7.6E-21

689

1,395 (11%)

hsa-mir-526bstar

GCACTTTC

NA

14.57

4.8E-22

746

1,450 (12%)

hsa-mir-93

GCACTTTG

1

12.99

1.4E-13

790

1,490 (12%)

hsa-mir-17

GCACTTTG

10

12.99

1.4E-13

790

1,490 (12%)

hsa-mir-20b

GCACTTTG

NA

12.99

1.4E-13

790

1,490 (12%)

hsa-mir-519d

GCACTTTG

NA

12.99

1.4E-13

790

1,490 (12%)

hsa-mir-520d-3p

AGCACTTT

NA

12.15

4.2E-11

796

1,496 (12%)

hsa-mir-520b

AGCACTTT

NA

12.15

4.2E-11

796

1,496 (12%)

hsa-mir-520e

AGCACTTT

NA

12.15

4.2E-11

796

1,496 (12%)

hsa-mir-372

AGCACTTT

NA

12.15

4.2E-11

796

1,496 (12%)

hsa-mir-520c-3p

AGCACTTT

NA

12.15

4.2E-11

796

1,496 (12%)

hsa-mir-520a-3p

AGCACTTT

NA

12.15

4.2E-11

796

1,496 (12%)

hsa-mir-3609

TCACTTTG

NA

10.2

9.3E-09

798

1,498 (12%)

3

hsa-mir-92a-1

GTGCAATA

4

13.59

4.8E-10

223

1,709 (14%)

hsa-mir-32

GTGCAATA

95

13.59

4.8E-10

223

1,709 (14%)

hsa-mir-92b

GTGCAATA

101

13.59

4.8E-10

223

1,709 (14%)

hsa-mir-92a-2

GTGCAATA

NA

13.59

4.8E-10

223

1,709 (14%)

hsa-mir-25

GTGCAATG

11

11.38

2.2E-09

239

1,722 (14%)

hsa-mir-363

GTGCAATT

130

11.33

1.6E-09

265

1,746 (14%)

hsa-mir-367

GTGCAATT

NA

11.33

1.6E-09

265

1,746 (14%)

4

hsa-mir-454

TTGCACTA

108

12.04

2.3E-04

298

1,904 (16%)

5

hsa-mir-101-2

GTACTGTA

12

11.87

1.7E-11

202

2,098 (17%)

hsa-mir-101-1

GTACTGTA

NA

11.87

1.7E-11

202

2,098 (17%)

hsa-mir-144

ATACTGTA

NA

9.83

8.3E-06

260

2,151 (18%)

Clustering is based on highly similar miRNA seeds (third column). Predictions are ordered based on the enrichment scores assigned by the motif analysis performed using mEAT. For each cluster prediction we report the expression rank (fourth column), the mEAT enrichment score (fifth column), the P-value estimate based on permuting the binding evidence assignment (100 draws) combined with a parametric fit to a Gaussian distribution (sixth column), the number of targets that represents the total number of regions with a match to at least one of the canonical seeds of the cluster members (seventh column), and the cumulative number of targets that corresponds to the union of the predicted targets of the current cluster with all others preceding it (eighth column). miRNAs that were not reported as expressed in Hafner et al. [7] were assigned 'NA' values; some of these are recently identified miRNAs not known at the time of measuring expression levels.

Corcoran et al. Genome Biology 2011 12:R79   doi:10.1186/gb-2011-12-8-r79