miRNA target prediction

Question

[glady]

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.

Answer 1

[Asaf]

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.

[glady]

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

[GenoMax]

Link fixed.