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.