biomaRt getBM function report some NA

Question

[Bastien Hervé]

I'm trying to get some entrez ids from some gene names using biomaRt

In my example below I have 2 genes Igha and Mlc1 for mus musculus

My version of biomaRt is biomaRt_2.38.0

library("biomaRt")
mart <- useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl")
getBM(attributes=c("ensembl_gene_id","mgi_symbol","entrezgene"), values = c("Igha", "Mlc1"), bmHeader = T, filters = "mgi_symbol", mart = mart)
#      Gene stable ID MGI symbol NCBI gene ID
#1 ENSMUSG00000095079       Igha           NA
#2 ENSMUSG00000035805       Mlc1       170790

I know that some Ensembl gene ID do not have Entrez gene ID ENSEMBL IDs 2 Entrez Gene IDs - what to do if no match?

But in this case, I'm able to find the Entrez gene ID from Ensembl

http://www.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000095079;r=12:113254830-113260236

Which is Refseq Gene ID 238447

Maybe Emily_Ensembl will have an answer :)

Answer 1

[Emily]

The gene listed on the gene page is not actually a proper external reference and doesn't come through BioMart. That comes through a different pipeline and it's not reliable and we're getting rid of it.

[Bastien Hervé]

So... No enrichment analysis for immunoglobulin genes in mus musculus ? I use enrichPathway which needs entrez gene ids.

[GenoMax]

Use Entrezdirect.

$ esearch -db gene -query "Mlc1 [gene] and 10090 [taxID]" | efetch 

1. Mlc1
Official Symbol: Mlc1 and Name: megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human) [Mus musculus (house mouse)]
Other Aliases: AW048630, BB074274, Kiaa0027-hp, LVM, MLC, VL, WKL1
Other Designations: membrane protein MLC1
Chromosome: 15; Location: 15 E3
Annotation: Chromosome 15 NC_000081.6 (88955884..88982691, complement)
ID: **170790**

$ esearch -db gene -query "Igha [gene] and 10090 [taxID]" | efetch 

1. Igha
Official Symbol: Igha and Name: immunoglobulin heavy constant alpha [Mus musculus (house mouse)]
Other Aliases: IgA, Igh-2
Other Designations: immunoglobulin heavy chain 2 (serum IgA)
Chromosome: 12; Location: 12 62.09 cM
Annotation: Chromosome 12 NC_000078.6 (113256204..113260236, complement)
ID: **238447**

Answer 2

[Bastien Hervé]

Using genomax 's comment

Here is my trick using esearch

biomart_genes <- getBM(attributes = c("external_gene_name", "entrezgene"), filters = "mgi_symbol", values = gene_list, bmHeader = T, mart = mart)
colnames(biomart_genes) <- c("hgnc_symbol","entrez_gene_id")

for (i in 1:nrow(biomart_genes)){
    if is.na(biomart_genes[i,"entrez_gene_id"])){
        term <- paste0(biomart_genes[i,"hgnc_symbol"]," [gene] and 10090 [taxID]")
        biomart_genes[i,"entrez_gene_id"] <- uid(esearch(term, db = "gene", rettype = "uilist", retmode = "xml", retmax = 1))
    }
}