Question: get gene targets from a specific microRNA
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gravatar for yotsawat pomyen
7.0 years ago by
yotsawat pomyen40 wrote:
Hi All, I'm trying to get lists of gene targets from specific microRNAs, namely the hsa-miRs and hsa-let-7s from the package targetscan.Hs.eg.db. So far, I can only see a way to do that by mapping all hsa-miRs into miR family names first, then get gene target list from mget(mir_family, revmap(targetscan.Hs.egTARGETS)). The problem is that some miR families include non-human miRs. I just want the targets of human miRs only. Cheers, Yot [[alternative HTML version deleted]]
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ADD COMMENTlink modified 7.0 years ago by James F. Reid120 • written 7.0 years ago by yotsawat pomyen40
Answer: get gene targets from a specific microRNA
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gravatar for James F. Reid
7.0 years ago by
James F. Reid120
James F. Reid120 wrote:
Hi Yot, > > Hi All, > > I'm trying to get lists of gene targets from specific microRNAs, namely the > hsa-miRs and hsa-let-7s from the package targetscan.Hs.eg.db. > > So far, I can only see a way to do that by mapping all hsa-miRs into miR > family names first, then get gene target list from mget(mir_family, > revmap(targetscan.Hs.egTARGETS)). The problem is that some miR families > include non-human miRs. I just want the targets of human miRs only. Your approach is correct: library("targetscan.Hs.eg.db") ## select human mirna humanMirnaIdx <- grep("hsa", mappedkeys(targetscan.Hs.egMIRNA)) humanMirna <- mappedkeys(targetscan.Hs.egMIRNA)[humanMirnaIdx] ## select seed-based families for human mirna humanMirnaFamilies <- unlist(mget(humanMirna, targetscan.Hs.egMIRBASE2FAMILY)) ## select targets of families humanMirnaTargets <- mget(humanMirnaFamilies, revmap(targetscan.Hs.egTARGETS)) names(humanMirnaTargets) <- humanMirna now you have a list of human mirna with their respective gene targets. Note that you will have some redundancy to care of. Namely that single mirna belonging to the same family will have the same target genes and also within a list of putative targets you will find some genes repeated because they match multiple time in the 3' UTR. It is expected for a seed-based family to have mirna that belong to other species. Best, J. > > Cheers, > > Yot
ADD COMMENTlink written 7.0 years ago by James F. Reid120
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