GO enrichment of miRNAs in WGCNA

Question

[msumaira36]

I am using wgcna to find hub miRNAs in cancer. I have successfully generated modules from my data. Problem is in GO enrichment of these modules. My code is:

allLLIDs = dbData[,1] 
##allLLIDs contains miRNA identifiers
GOenr = GOenrichmentAnalysis(moduleColors, allLLIDs, organism = "human", nBestP = 10);
Error : Error in labels[keepEC, , drop = FALSE] : subscript out of bounds

my miRNA identifiers are in form: hsa-miR-21 etc. Please help me in fixing this problem .. Thankyou..

[Lluís R.]

Gene Ontologies are not for micro RNAs. But you could select the GO of the genes those miRNA target to.

[msumaira36]

thankyou for your reply..

Answer 1

[Kevin Blighe]

Use miRNAtap to identify the gene targets of the micro RNAs. Then use topGO and KEGGprofile to identify Gene Ontology (GO) terms and KEGG pathways that are statistically significantly enriched by these gene targets.

Kevin