Question: Finding miRNA motifs from Exome sequencing
1
gravatar for bharata1803
3.0 years ago by
bharata1803400
Japan
bharata1803400 wrote:

Hello,

I got a suggestion from my supervisor to check cancer data and miRNA effect. All I can get from NCBI GEO is 7 pairs of RNA-seq data of normal-tumor cell and 8 pairs of whole exome seq data also from normal-tumor cell.

After reading several source and try 1 of the motif finding of miRNA in UTR, I have an idea for checking the relation of miRNA and gene expression. My idea is like this:

Check the miRNA binding motifs from the sample's 3'UTR. From this, I will get the possible miRNA which bind with mRNA for specific sample in a specific gene. Then, I will combine the gene expression data with the predicted miRNA which bind to those mRNA of those genes.

Is it possible to do that? I will need to get 3'UTR sequence from every samples which I think I can get from whole exome seq. Is it possible to get the 3'UTR from whole exome seq?

mirna exome-seq sequence • 1.0k views
ADD COMMENTlink written 3.0 years ago by bharata1803400

Any update on this? I also wonder if exome sequencing contains 3' UTR regions

ADD REPLYlink written 4 months ago by -_-740

the answer is no, exome seq only sequence known/targeted exon region

ADD REPLYlink written 3 months ago by bharata1803400
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