Are there good reference for miRNA microRNA pathway analysis in R following edgeR run?

Question

[Björn]

I have a list of 5 miRNAs for which I would like to perform pathway analysis in relation to cancer. In literatures, KEGG, TargetScan; DIANA-miPATH are suggested. However, I am unable to find literature with r-code which makes easier to learn and also save lots of time.

Answer 1

[Kevin Blighe]

Hi Björn, perhaps the answers here will help: miRNA target genes prediction.

Answer 2

[brianj.park]

Hi,

Late reply but for anyone looking for resources: miRNAtap (http://bioconductor.org/packages/release/bioc/html/miRNAtap.html) from Bioconductor is a good place to look for enrichment analysis after differential expression for miRNAs. It takes miRNA input and gives you a consolidated data frame of gene targets from sources such as DIANA, miRNADA, and TargetScan. You can then take these entrez gene IDs and their rank scores into topGO for overrepresentation analysis. Their vigenette goes through this workflow.