Question: How to map miRNA to transcripts of targeting genes ?
1
gravatar for jack
4.8 years ago by
jack750
Germany
jack750 wrote:

Hi,

 

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 3.6 years ago by Bade40 • written 4.8 years ago by jack750
1

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 4.7 years ago • written 4.7 years ago by Manvendra Singh2.0k
0
gravatar for Renesh
4.6 years ago by
Renesh1.6k
United States
Renesh1.6k wrote:

Refer this link: http://mirnablog.com/microrna-target-prediction-tools/

It provides several tool for miRNA target prediction.

ADD COMMENTlink written 4.6 years ago by Renesh1.6k
0
gravatar for Bade
3.6 years ago by
Bade40
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 - https://github.com/atulkakrana/sPARTA.github

Link to paper- http://nar.oxfordjournals.org/content/42/18/e139

Bade

ADD COMMENTlink written 3.6 years ago by Bade40
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