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Finding miRNA motifs from Exome sequencing
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14 months ago
bharata1803 • 420


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?

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

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


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