Hi,

I am trying to annotate a list of differentially expressed genes output by DESeq2, with ensembl IDs, gene symbols and gene descriptions. I originally aligned and mapped the reads using a .gtf annotation file from NCBI, so the DESeq2 gene list appears to have a list of Entrez gene ID and locus tags as identifiers.

I constructed the biomaRt query below and whilst it runs without error, it returns no hits. This is despite the few genes I have checked on NCBI also having an equivalent ensembl ID.

I have tried reading through the "Accessing Ensembl annotation with biomaRt" file for information but couldn't find the answer I was looking for.

Does anyone have any advice as to how to get my query to work?

Thanks,

Alan

ensembl_nilo <- useMart("ensembl", dataset = "oniloticus_gene_ensembl")

a <- read.delim("Kidney-Allgenes-DESeq2_ID.txt", head=TRUE)
head(a)
# gene
# 1  KEH09_p01
# 2  KEH09_p02
# 3  KEH09_p03
# 4  KEH09_p04
# 5  KEH09_p05
# 6  KEH09_p06

b <- getBM(attributes = c("ensembl_gene_id", "entrezgene_id", "entrezgene_accession"),     
                          filters = "entrezgene_id",
                          values = a$gene,         
                          mart = ensembl_nilo)
b
# [1] ensembl_gene_id      entrezgene_id        entrezgene_accession
# <0 rows> (or 0-length row.names)