Gene enrichment analysis - How to get the gene names in Entrez id's?
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3.1 years ago
bionewbie • 0

I am trying to perform GO analysis and I would like to derive the gene names that are associated with upregulation for log fold change of 1 and above. I am right now getting BP id, value, count, term etc. but I need the gene name as well. Also I am trying to do Kegg pathway analysis similarly and get the gene names in that as well. GO Enrichment analysis using GOstats

library(GO.db)

library(GOstats)

selectedGenes = unique(resSig[resSig$log2FoldChange>1,'entrez'])  # upregulated genes

universeGenes =  unique( mapIds(org.Hs.eg.db,
                     keys= res$ensembl,
                     column="ENTREZID",
                     keytype="ENSEMBL", #Out ID is ENSMBL
                     multiVals="first")
                    )


 hgCutoff <- 0.001

params <- new("GOHyperGParams",
     geneIds=selectedGenes,
     universeGeneIds=universeGenes,
     annotation="org.Hs.eg.db",
     ontology="BP",
     pvalueCutoff=hgCutoff,
     conditional=FALSE,
     testDirection="over")

hgOver <- hyperGTest(params)
summary(hgOver)
Bioconductor Geneenrichment RNAseq genomics • 610 views
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