Ensembl_Gene_Id To Entrezgene With Biomart

Question

[pchiang5]

Hello,

I have a tab delimited txt file with ensembl_gene_id in the first column. The other columns represent the counts of RNA-seq alignment. Is that possible to convert those IDs to entrezgene with biomaRt package in R? Thanks.

Answer 1

[Devon Ryan]

This isn't a Biomart method, but uses the various org.XX.eg.db packages in R (org.Mm.eg.db in this example).

#Loading data not shown, but in this example it's stored in "d"
library(org.Mm.eg.db)
egENSEMBL <- toTable(org.Mm.egENSEMBL)
m <- match(d$EnsemblID, egENSEMBL$ensembl_id)
d$EntrezID <- egENSEMBL$gene_id[m]

The match() functions are quite useful. You can add gene symbols and names in a similar way.

Edit: I should mention that Ensembl IDs are generally more useful than Entrez IDs, at least in my experience.

[pchiang5]

Thanks you dpryan79！

I was not able to load the library(org.Mm.eg.db). The R replied "there is no package called "org.Mm.eg.db", although loading "org.Hs.eg.dg" is OK. Did I miss something like dependencies to load the database? Or is there any other alternative databases for the purpose? Thanks again.

[Devon Ryan]

org.Mm.eg.db was just an example, use whatever is appropriate to your species of interest. Also, you have to install the relevant package before you can use it.

[pchiang5]

Finally I got it done by your match() function and biomaRt database.

Millions of thanks！

Answer 2

[Neilfws]

Is that possible? Yes, it is.

A little more detail: use ensembl_gene_id as the filter and as a minimum, entrezgene and ensembl_gene_id as the attributes.

[pchiang5]

Thank you Neilfws.

I am still having hard time loading library(org.Mm.eg.db). It is confusing since loading the human version 'org.Hs.eg.db' showed no problem.