How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
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Entering edit mode
7 months ago
bioinfo ▴ 150

Hello,

I did DESeq2 on my samples and I have a list of DEGs that I would like to do kegg pathway analysis on. For DESeq2 I used biomart and tximport to assign external gene names to my genes. My plan is to use biomart to assign entrez IDs to the gene names and then use gage for the kegg pathway analysis. I created my t2g object like shown below,

mart <- biomaRt::useMart("ensembl", "hsapiens_gene_ensembl")
t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
                                     "external_gene_name", "entrezgene_id"), mart = mart)

I decided to check that every gene name has a unique entrez ID. However, I saw that I have 126 genes with more than one entrez ID. 125 of them are not statistically significant so I was not planning to use them for kegg. However, one of the genes has a p value of 0.03 so I was interested in it. There are 2 entrezIDs associated with it. What can I do about it? Should I run KEGG twice? One time with each entrez ID?

Thank you

biomart kegg deseq2 • 348 views
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