Search
Question: Finding orthologous human/mouse ENSEMBL IDs
1
gravatar for Keith Hughitt
12 months ago by
Keith Hughitt110
United States
Keith Hughitt110 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

 

 

 

 

ADD COMMENTlink modified 12 months ago • written 12 months ago by Keith Hughitt110
1
gravatar for Keith Hughitt
12 months ago by
Keith Hughitt110
United States
Keith Hughitt110 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   

 

ADD COMMENTlink modified 12 months ago • written 12 months ago by Keith Hughitt110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 235 users visited in the last hour