I would like to convert murine ensembl gene ids to human ensemble gene ids using biomaRt.

library(biomaRt)
mart1 <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
mart2 <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
genes.ensembl.biomart <- getLDS(attributes = c("ensembl_gene_id"), filters = "ensembl_gene_id", values = genes.ensembl.murine, mart = mart1, attributesL = c("ensembl_gene_id"), martL = mart2)

To keep the order I used match.

genes.ensembl <- data.frame (murine_ensembl = genes.ensembl.murine)
genes.ensembl$human_ensembl <- genes.ensembl.biomart[match(genes.ensembl[,1], genes.ensembl.biomart[,1]),2]

genes.ensembl.murine is a vector of length 14040.

     head(genes.ensembl.murine, 20)
 [1] ENSMUSG00000025902 ENSMUSG00000033845 ENSMUSG00000025903 ENSMUSG00000033813
 [5] ENSMUSG00000033793 ENSMUSG00000025907 ENSMUSG00000051285 ENSMUSG00000061024
 [9] ENSMUSG00000025911 ENSMUSG00000045210 ENSMUSG00000025915 ENSMUSG00000098234
[13] ENSMUSG00000025917 ENSMUSG00000056763 ENSMUSG00000067851 ENSMUSG00000048960
[17] ENSMUSG00000016918 ENSMUSG00000005886 ENSMUSG00000025935 ENSMUSG00000025937

The resulting data frame has 1396 missing values.

head(genes.ensembl[whichis.na(genes.ensembl[2])),], 10)
        murine_ensembl human_ensembl
12  ENSMUSG00000098234          <NA>
24  ENSMUSG00000043716          <NA>
43  ENSMUSG00000026064          <NA>
82  ENSMUSG00000073702          <NA>
85  ENSMUSG00000091937          <NA>
133 ENSMUSG00000025980          <NA>
134 ENSMUSG00000073676          <NA>
137 ENSMUSG00000097649          <NA>
146 ENSMUSG00000026035          <NA>
156 ENSMUSG00000097573          <NA>

Ensembl says ENSMUSG00000098234 is Snhg6 (http://www.ensembl.org/Musmusculus/Gene/Summary?g=ENSMUSG00000098234;r=1:9941959-9944118) , and the human orthologue is ENSG00000245910 (http://www.ensembl.org/Homosapiens/Gene/Summary?g=ENSG00000245910;r=8:66921684-66926398). However, using biomart on ensembl.org also doesn't find the human orthologue for ENSMUSG00000098234 .

Can anybody help me to convert the missing 1396 genes? Is it a problem with biomaRt or with ensembl.org?

Thank you very much. Mischko

When you go to either of the pages you link, while they do show the same gene symbol, they do not have a link for any orthologs under the comparative genomics section, indicating that EBI/EMBL do not think these two genes are orthologs.

As a counter example, consider Sox17, which lists 24 primate orthologs, including SOX17.

Without looking at all 1396 genes, I cannot say if that follows for all of them, but in general I haven't ever found different results when going to ensembl.org than what I already got from the Biomart server, which makes sense, given that they are based on the same underlying database.