What gene mouse IDs are these?
I am working with a scRNA-seq count matrix from a paper whose genes have names as follow:
213 1700022K14Rik
214 1700022N22Rik
215 1700022P22Rik
216 1700023E05Rik
217 1700023F06Ri
...
1802 AC158802.1
1803 AC158997.1
1804 AC161214.1
...
18245 Nkg7
18246 Nkiras1
18247 Nkiras2
18248 Nkpd1
18249 Nkrf
...
4206 Ccdc67
4207 Ccdc68
4208 Ccdc69
4209 Ccdc7
4210 Ccdc70
4211 Ccdc7
...
12207 Gm25168
12208 Gm25172
12209 Gm25173
12210 Gm25175
...
26864 n-R5s29
26865 n-R5s3
26866 n-R5s30
26867 n-R5s33
Does anybody know what kind of gene names are these? Is there an easy way to convert them to Ensembl stable IDs? (example: ENSMUSG00000084573)
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1 answer
These are MGI gene symbols. Here is a way to convert in R using biomaRt. This code snipped will return a table with all Ensembl genes for mice providing a lookup table that you can use (may take 1min to complete):
library(biomaRt)
genes <- biomaRt::getBM(attributes = c("ensembl_gene_id", "mgi_symbol"),
mart = useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl"))
head(genes)
ensembl_gene_id mgi_symbol
1 ENSMUSG00000064336 mt-Tf
2 ENSMUSG00000064337 mt-Rnr1
3 ENSMUSG00000064338 mt-Tv
4 ENSMUSG00000064339 mt-Rnr2
5 ENSMUSG00000064340 mt-Tl1
6 ENSMUSG00000064341 mt-Nd1
From there you can pull any gene you want. Something like:
wanted <- c("Spi1", "Gata3", "Nkg7")
genes[genes$mgi_symbol %in% wanted,]
ensembl_gene_id mgi_symbol
1430 ENSMUSG00000004612 Nkg7
16176 ENSMUSG00000015619 Gata3
34659 ENSMUSG00000002111 Spi1
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did you try biomart ?