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GO enrichment of miRNAs in WGCNA

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..

wgcna go enrichment
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updated by Kevin Blighe Kevin Blighe • written by msumaira36 • msumaira36

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

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written by Lluís R. Lluís R.

1 answer

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

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written by Kevin Blighe Kevin Blighe

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