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?
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.
Refer to this link
It provides several tool for miRNA target prediction.
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
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