> Hi All,
> I'm trying to get lists of gene targets from specific microRNAs,
> 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
> family names first, then get gene target list from mget(mir_family,
> revmap(targetscan.Hs.egTARGETS)). The problem is that some miR
> include non-human miRs. I just want the targets of human miRs only.
Your approach is correct:
## 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,
## select targets of families
humanMirnaTargets <- mget(humanMirnaFamilies,
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
belonging to the same family will have the same target genes and also
a list of putative targets you will find some genes repeated because
match multiple time in the 3' UTR.
It is expected for a seed-based family to have mirna that belong to