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Table 2 Summary of the top de novo miRNA target predictions based on the Argonaute PAR-CLIP data

From: PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence 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%)
  1. 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.