Table 1

Summary of motif matches in the different PAR-CLIP datasets

Number of motif matches

Total nucleotides

Signal-to-noise

Number of interaction sites with motif/Total number of interaction sites


Argonaute (top 20 expressed miRNAs)

PARalyzer

3,933

207,334

2.68

3,041/11,353

Hafner et al. (CCRs)

4,106

301,227

1.92

3,090/6,796

Background (3' UTRs)

131,741

18,602,068

-

-

PUM2

PARalyzer

1,262

127,168

60.28

1,344/6,990

Hafner et al.

1,371

200,228

41.59

1,290/5,668

Background

113,478

689,309,457

-

-

QKI

PARalyzer

3,001

155,237

19.19

2,771/5,361

Hafner et al.

2,593

127,201

20.24

2,079/3,903

Background

694,229

689,309,457

-

-

IGF2BP1

PARalyzer

31,507

1,718,152

1.35

24,758/55,831

Hafner et al.

51,429

3,739,750

1.01

32,303/59,784

Background

9,343,410

689,309,457

-

-


The Argonaute results are specific to only the 3' UTR region and contain only non-redundant seed matches. Summary of the motif matches for Pumilio2 (PUM2), Quaking (QKI), and Insulin-like growth factor 2 binding protein 1 (IGF2BP1) were generated from the analysis of the full transcript of all genes, including 5' UTRs, 3' UTRs, introns and coding regions. The Hafner et al. [7] crosslink-centered regions (CCRs) are those provided in their manuscript.

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

Open Data