What gene mouse IDs are these?
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20 months ago

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)

gene mouse ID • 386 views
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Entering edit mode

Is there an easy way to convert them to Ensembl stable IDs?

did you try biomart ?

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Entering edit mode
20 months ago
ATpoint 65k

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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