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miRNA target prediction

Hello all,

I'm working on Human miRNA's, and I'm trying to predict miRNA targets in coding and non-coding genes. The algorithms(MiRanda, RNAhybrid, PITA) produce a lot of false positives and also there results differ significantly. So, now I use some online databases(TargetSCAN, starBase, miRtarbase, etc). However, I'm having some doubts while using these databases;

1) Do the miRNA's have different targeting genes in different cell lines(HUVEC, HELA, etc)? 2) Does the miRNA's have an opposite effect on its targets in Tumor and normal cells?

Thank you.

rna-seq
• 1,635 views • link
updated by Asaf Asaf • written by glady glady

1 answer

  1. The prediction will give you an answer to the question is there a potential binding between the miRNA and mRNA. The regulation depends on a lot of factors like mRNA levels, miRNA lavels, AGO abundance, other miRNAs in the cell, so yes, it will vary between cell lines or cell types. (See this paper for instance: https://www.ncbi.nlm.nih.gov/pubmed/24853754 )
  2. I might be but I suggest you'll look for papers about it. I don't know if it was recorded.
• 0 views • link
updated by GenoMax GenoMax • written by Asaf Asaf

Thank you very much for the suggestion, sir. Unfortunately, the link for the paper is broken. Can you please share it again?

• 0 views • link
written by glady glady

Link fixed.

• 0 views • link
written by GenoMax GenoMax

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