fetch miRNA target and map them to pathways using R/bioconductor
cited from:
Bioconductor Digest, Vol 108, Issue 28
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here is the outline on how to do this using the miRNA predictedconserved targets using targetscan in Human (it can also be done in Mouse).myMir <- "hsa-mir-17"# 1. to find targets we need to use the mature form of the mirna# we can do this using 'mirbase.db'require("mirbase.db") || stop("Could not load package 'mirbase.db'")## inspect the mature forms for this particular miRNAprint(get(myMir, mirbaseMATURE))##Accession: MIMAT0000070## ID: hsa-miR-17## Start: 14## End: 36## Evidence: experimental## Experiment: cloned [2,5-8], Northern [4]####Accession: MIMAT0000071## ID: hsa-miR-17*## Start: 51## End: 72## Evidence: experimental## Experiment: cloned [1,5,7-8], Northern [1]## select the first onemyMature <- matureName(get(myMir, mirbaseMATURE))[1]# 2. find the targets of this mature mirna using targetscanrequire("targetscan.Hs.eg.db") || stop("Could not load package", "'targetscan.Hs.eg.db'")## get the seed-based family associated with this mature mirnamyMirFam <- get(myMature, targetscan.Hs.egMIRBASE2FAMILY)## retrieve targets (as NCBI Gene IDs)myMirTargets <- get(myMirFam, revmap(targetscan.Hs.egTARGETS))##length(myMirTargets)##[1] 1114## 3. map target genes to KEGG pathwaysrequire("org.Hs.eg.db") || stop("Could not load package", "'org.Hs.eg.db'.")myMirTargetsKegg <- mget(myMirTargets, org.Hs.egPATH)##sum(!is.na(myMirTargetsKegg))##[1] 315## optional for convenience, add KEGG pathway namesrequire("KEGG.db") || stop("Could not load package 'KEGG.db'")## using only the entries with a KEGG idmyMirTargetsKeggNames <- lapply(myMirTargetsKegg[!is.na(myMirTargetsKegg)], function(i) mget(i, KEGGPATHID2NAME))Note that since KEGG is no longer public and that the BioConductorpackage will soon be considered deprecated you could use the'reactome.db' package instead for mapping pathways. Just replace thestep 3. above by a call to:mget(myMirTargets, reactomeEXTID2PATHID, ifnotfound=NA)I'll leave finding the pathway names as an exercise ;-)
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