Question: miRNA target prediction
0
gravatar for glady
4 months ago by
glady260
glady260 wrote:

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 • 156 views
ADD COMMENTlink modified 4 months ago by Asaf8.1k • written 4 months ago by glady260
0
gravatar for Asaf
4 months ago by
Asaf8.1k
Israel
Asaf8.1k wrote:
  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.
ADD COMMENTlink modified 4 months ago by genomax85k • written 4 months ago by Asaf8.1k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by glady260

Link fixed.

ADD REPLYlink written 4 months ago by genomax85k
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