Question: Detecting miRNA effect from RNA-seq
gravatar for bharata1803
4.5 years ago by
bharata1803460 wrote:

Hello all,


So, my supervisor wants me to check the effect of miRNA in RNA-seq data for tumor and non-tumor experiment data. The theory is miRNA is a possible cause of up/down regulation of a gene. I am totally new to miRNA and I need some help understanding this. What I have noow is the FASTA file of miRNA from, FASTA file from the RNA-seq experiment (7 normal-tumor pair) and the expression of each gene for each sample (use Salmon to get the expression level from FASTA file). My questions are:

1. Are there already known which miRNA binds to which mRNA? I imagine it is like a KEGG pathway database which we can see a gene is regulated by several genes. If not, can I derived the information with the miRNA sequence database I downlooaded?

2. If miRNA binds to the mRNA, will it observable in the RNA-seq data? I mean, imagine we have 1 gene with 2 conditions, 1 normal and 1 is bounded with miRNA. Is the miRNA-bound mRNA expression differ with the normal ones assuming no other difference? 


Thank you!

rna-seq • 1.6k views
ADD COMMENTlink written 4.5 years ago by bharata1803460


1. Some databases combining experimental evidences and in silico predictions of miRNA-mRNA interactions exist. miRWalk and DIANA microT are good start. You can also derive your own predictions using various in silico prediction tools (TargetScan, miRanda, RNAhybrid,...).

2. I don't have enough expertise to answer the second question. The level of mRNA will be different between your normal and miRNA-mRNA condition but you won't be able to attribute for sure the difference to the interaction with the a particular miRNA in a simple tumor vs control study. 

ADD REPLYlink written 4.5 years ago by VHahaut1.1k
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