Which miRNA arm to select for target prediction, 3p or 5p?

Question

[Tusharika]

Hello!

I am working on Cancer Data to find differential expressions of miRNAs between Tumor and Normal Samples. Further, I want to predict targets for Differentially expressed miRNAs using miRDB but it asks me to select between the 3p and 5p arms. Which one should I select?

For example:

I am inputting "hsa-mir-196b" in miRDB, it asks me to select from 3p and 5p http://www.mirdb.org/cgi-bin/search.cgi

Which one should I select?

[Buffo]

How did you identify those "Differentially expressed miRNAs"?. A single miRNA precursor can originate different mature miRNAs, so, if your method of identification doesn't have the resolution to identify mature miRNAs, I suggest you select both.

[Tusharika]

Thanks! I have used the miRNA dataset from XenaBrowser and ran the Differential Expression pipeline on it using the DESeq2 Bioconductor package.

Further, I want to ask if hsa-mir-196a-1 is the same as hsa-mir-196a-3p. In my DEMs, I have the name written as hsa-mir-196a-1.

[Buffo]

Take a look at this miRBase result for hsa-mir-196a. As you can see, the precursor can produce very different mature miRNAs with similar names.

[Tusharika]

Yes! But can you please elaborate? I am not able to understand.

[Buffo]

miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants