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.
lincRNA & lncRNA
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:
- Use columns 3, 4, and 13
- 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
- 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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