Question

Go terms for Ensemble gene list

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Raquel • 0

@raquel-22521

Last seen 5.0 years ago

Hi all,

could anybody help me adding Go-ID terms to my ensemble gene list please? My object (diffexpr_results) looks like this: x Gene baseMean log2FoldChange

1 ENSMUSG00000004552 111,80117 1,0805015

2 ENSMUSG00000057897 627,24564 -1,1564159

3 ENSMUSG00000026347 146,49072 -0,7324188

4 ENSMUSG00000071796 85,67142 0,777473

5 ENSMUSG00000044337 15,15884 1,6598731

6 ENSMUSG00000076940 35,37653 -1,0034472

How can I add a Go-ID column? I tried: mouse.ensembl<- useMart("ensembl") mouse.ensembl<- useDataset("mmusculusgeneensembl", mart=mouse.ensembl) go <- getBM(attributes = c("ensemblgeneid", "goid"), + filters = "ensemblgeneid", + values = diffexprresults, + mart = mouse.ensembl)

Thanks a lot

go • 736 views

ADD COMMENT • link 4.9 years ago Raquel • 0

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What happened when you tried the biomaRt example?

ADD REPLY • link 4.9 years ago Mike Smith ★ 6.6k

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Also, do note that Ensembl gene ID -> GO ID is a one-to-many mapping, so it's not so simple to add to a table like that. For example, your first gene:

> library(biomaRt)
> mart <- useEnsembl("ensembl","mmusculus_gene_ensembl", mirror = "useast")
> getBM(c("ensembl_gene_id","go_id"), "ensembl_gene_id", "ENSMUSG00000004552", mart)
      ensembl_gene_id      go_id
1  ENSMUSG00000004552 GO:0006508
2  ENSMUSG00000004552 GO:0004190
3  ENSMUSG00000004552 GO:0016540
4  ENSMUSG00000004552 GO:0016787
5  ENSMUSG00000004552 GO:0008233
6  ENSMUSG00000004552 GO:0042803
7  ENSMUSG00000004552 GO:0005768
8  ENSMUSG00000004552 GO:0030163
9  ENSMUSG00000004552 GO:0019886
10 ENSMUSG00000004552

You could concatenate all those GO IDs with commas or something, but a GO ID isn't really useful as it is (you don't mention your use case), and in general for eyeballometric analyses you would rather the Term, as the ID is pretty cryptic.

ADD REPLY • link 4.9 years ago James W. MacDonald 67k