RNA22 full sets of predictions

View this predictions in our RNA22 visualization tool | Use RNA22 to create your own predictions with our RNA22 dynamic prediction tool

If you use any of the below please cite: Miranda, KC et al (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes Cell, 126, 1203-1217, 10.1016/j.cell.2006.07.031.

From this page you can download the full sets of miRNA target predictions created with RNA22 and used by our RNA22 visualization tool.

1940 Downloads
411 Downloads
353 Downloads
488 Downloads
541 Downloads
562 Downloads
441 Downloads
436 Downloads
320 Downloads

 

How to read the files and extract coordinates

Suppose that you have the following line

hsa_miR_xxxx ENSG00000048028_ENST00000003302_11_-1 **cDNA_FROM_3557_TO_3902 321 test.seq -23.799999 GTCTCTCTCCTTTCTTTT GAAAGAGAGCTGAGTGTG ..(.(((..((((((((( )))))))))..))).).. 13 13 18 0 0 quality_estimate(higher-is-better)= 1.437500 3'UTR

Each line of the miR file is a predicted target site for that miR.
Column 1 (and filename): name of miR
Column 2: Ensembl Gene ID, Ensembl Transcript ID, chromosome, and strand (-1 for reverse, 1 for sense)
Column 3 & 4: Both of these columns are used to calculate the start/end location of the predicted target site that the miR targets – see section below.
Column 5: always test.seq (you can ignore this)
Column 6: binding energy in -Kcal/mol of the predicted heteroduplex between microRNA and the targeted messenger RNA
Column 7: target site sequence
Column 8: miR sequence
Column 9-10: shows you where the base pairings are for the formed heteroduplex
Column 11 & 12: always the same, the number of paired nucleotides in the heteroduplex
Column 13: the span/length of the predicted target (will be used to calculate the start/end location of the predicted target site that the miR targets – see section below)
Column 14-15: please ignore and do not use
Column 16: for RNA22v1.0, this column (quality_estimate) should be ignored.  For RNA22v2.0 this column represents the p-value.  The p-value represents the likelihood that the target site loci is random. That is, a lower p-value represents a greater chance that the loci contains a valid MRE
Column 17: region information (5′UTR, CDS, 3′UTR) for the predicted target site. Please note, a predicted target could overlap in both parts in which both parts will be specified

To calculate the local (1-based index) coordinates (These coordinates are relative to the start of the cDNA of the transcript) of the predicted target site:

  1. Use columns 3, 4, and 13
  2. The 4th column is an offset. So for the example above:
    • the start location is 3557 (from column 3) + 321 (from column 4) = 3878
    • the end location is 3557 (from column 3) + 321 (from column 4) + 18 (from column 13) – 1 = 3895

References

  1. Miranda, KC et al (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes Cell, 126, 1203-1217, 10.1016/j.cell.2006.07.031

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