I have 3 exomes results (VCF files), I would like to study variants (SNP, INDEL) that can affect the miRNAs, which are related to a complex disease (Schizophrenia). What is the best way to assess the effects of variants on miRNAs and how can I link between the damaged miRNAs and Schizophrenia. Can I find a help or advice please?
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$\begingroup$ I assume that you want a bioinformatician approach, not an experimental one, and that depends on the data you have (or you can obtain). For instance, how do you measure the damaged miRNAs? What data do you already have? $\endgroup$– llrsJul 23, 2018 at 10:47
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$\begingroup$ Do you want effects on miRNAs, or effects on their targets? $\endgroup$– Ian SudberyJul 24, 2018 at 10:48
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I would run them through the Ensembl VEP, which will tell you which genes they hit and the effect they have on them. Then I would filter by consequence "mature_miRNA_variant", which will find you all the variants in your file that fall in the mature miRNAs. Or you could filter instead by the gene biotype "miRNA" which will tell you if the variants fall anywhere in the miRNAs (which will include the full stem loop structure). I would then export the list of miRNAs and try to find out about their targets using miRbase.
