Question: How to map miRNA to transcripts of targeting genes ?
gravatar for jack
6.0 years ago by
jack810 wrote:



I have set of experimentally validated miRNA-gene interactions. I jut have information about the miRNA-Gene binding. but I want to know that miRNA to which transcripts or isoforms of targeting gene binds.


Would someone help me in this case ?

ADD COMMENTlink modified 4.8 years ago by Bade40 • written 6.0 years ago by jack810

I am just guessing that once you have found anti-correlation between the expression levels of miRNA and target genes, and seed is also pairing on 3'UTR then you might see whether , there is any specific isoform which is anticorrelated in sharp contrast with other isoforms of same gene.

PS: This is just a guess.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Manvendra Singh2.1k
gravatar for Renesh
5.8 years ago by
United States
Renesh1.9k wrote:

Refer this link:

It provides several tool for miRNA target prediction.

ADD COMMENTlink written 5.8 years ago by Renesh1.9k
gravatar for Bade
4.8 years ago by
United States
Bade40 wrote:

You can try sPARTA, if working on plants. It's very fast and sensitive to secondary structures that miRNA and target form -

Link to paper-


ADD COMMENTlink modified 8 months ago by RamRS28k • written 4.8 years ago by Bade40
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