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
Which is Refseq Gene ID 238447
Maybe Emily_Ensembl will have an answer :)
So... No enrichment analysis for immunoglobulin genes in mus musculus ? I use enrichPathway which needs entrez gene ids.
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**
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))
}
}
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