Question: Finding orthologous human/mouse ENSEMBL IDs
1
2.4 years ago by
Keith Hughitt120
United States
Keith Hughitt120 wrote:

Greetings,

I was wondering if someone might be able to help suggest a good way to generate a mapping of human/mouse orthologs, using ENSEMBL gene IDs?

I found a R function for mapping mouse genes to homologous human genes ? which pointed me to the inpIDMapper function in the AnntoationDbi package. The example usage shows how this function can be used to map a gene-indexed list of UniProt protein IDs, however, it's not clear whether this can be adapted for use with ENSEMBL gene ID's.

For example:

    human_ids <- c('ENSG00000109339', 'ENSG00000129990', 'ENSG00000132854', 'ENSG00000148204')
human_ids <- setNames(as.list(human_ids), human_ids)
mouse_ids <- inpIDMapper(human_ids, 'HOMSA', 'MUSMU', srcIDType='EG')

Results in an error:

    Error in names(destIDs) <- dnames : attempt to set an attribute on NULL
Calls: inpIDMapper       

Does anyone have a suggestion about how to go about generating such a mapping, using either this or another function?

Any help would be greatly appreciated.

Thanks!

Keith

modified 2.3 years ago • written 2.4 years ago by Keith Hughitt120
Answer: Finding orthologous human/mouse ENSEMBL IDs
2
2.3 years ago by
Keith Hughitt120
United States
Keith Hughitt120 wrote:

In case it helps anyone else, I was able to solve this using the second method suggested in the earlier post -- biomaRt's "getLDS()" function:

    mart1 = useMart("ensembl", dataset="hsapiens_gene_ensembl")
mart2 = useMart("ensembl", dataset="mmusculus_gene_ensembl")

human_ids <- c('ENSG00000109339', 'ENSG00000129990',
'ENSG00000132854', 'ENSG00000148204')

# human / mouse
getLDS(attributes=c("ensembl_gene_id"),
filters="ensembl_gene_id", values=human_ids, mart=mart1,
attributesL=c("ensembl_gene_id"), martL=mart2)

Gene.stable.ID   Gene.stable.ID.1
1 ENSG00000109339 ENSMUSG00000046709
2 ENSG00000132854 ENSMUSG00000035407
3 ENSG00000148204 ENSMUSG00000035403
4 ENSG00000129990 ENSMUSG00000004961