Can you do KEGG analysis in R without Entrez I.D.s
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Entering edit mode
9 months ago
devarts ▴ 20

Hi All. I've another newbie question for you. I've done RNAseq analysis in R for a set of organisms of the yeast species Yarrowia lipolytica strain CLIB122, with Ensembl IDs. I'd also like to do some KEGG ontology analysis. The tools that I have used for KEGG and GO analysis in the past (KEGGa (part of EdgeR) and fgSEA) require that Entrez I.D.s be used. Is this common for gene set analysis tools? Do they all need Entrez I.D.s? Are there tools/ packages that do not require Entrez I.D.s that can be used for KEGG? Which would you reccomend? It would be nice if they are R packages, but I could use other types of tools.

I found a biomart mart that I can use for Y. lipolytica, but it does not have an entrez attribute. Might any of you knowledgable bioinformaticians have a way that I could get around this. Could it be that there is simply not an Entrex I.D. list for Yarrowia lipolytica or other yeasts?

ensembl_fungi <- useMart(host = "https://fungi.ensembl.org",biomart = "fungi_mart", port = 443)
dataset <- "ylipolytica_eg_gene"
mart <- useDataset(dataset = dataset, ensembl_fungi)

Entrez KEGG R RNA-Seq biomaRt • 279 views