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?