Question: convert mouse genes to human ortholog
0
gravatar for bsr
3.8 years ago by
bsr0
United States
bsr0 wrote:

Anyone knows how to convert mouse genes to human ortholog to feed CMAP (Broad connectivity map)? Thanks!

 

rna-seq ortholog • 3.2k views
ADD COMMENTlink modified 3.8 years ago by Malcolm.Cook1.0k • written 3.8 years ago by bsr0
2
gravatar for Malcolm.Cook
3.8 years ago by
Malcolm.Cook1.0k
kansas, usa
Malcolm.Cook1.0k wrote:

It is not fully clear to me from your question what kind of mouse gene identifiers you have in hand.  Are the NCBI gene ids?  

If so, NCBI's homologene can be used to map them to gene ids in human that CMAP can accept.

Alas, at the NCBI web site, this can be done only one-at-a-time.

Enter stage left: Entrez Direct: E-utilities on the UNIX Command Line  which below looks up the homologene entry of two NCBI (mouse) gene IDs and outputs a table with two rows for each input geneID, one for each organism, which lists the homologene entry's ID followed by TaxonName and the id in that taxon.

echo -e "15394\n54624" | epost -db gene | elink -target homologene | efetch -format docsum | xtract -pattern DocumentSummary -HGID Id -block HomoloGeneData -match 'TaxName:Mus Musculus' -or 'TaxName:Homo Sapiens' -pfx "\n" -element '&HGID',TaxName,GeneID

5441    Homo sapiens    54623    
5441    Mus musculus    54624

4032    Homo sapiens    3198    
4032    Mus musculus    15394

Pipe the above into `| grep Homo | cut -f 3`to get just the human gene IDs.

Note:

 - there is no guarantee on order or results agreeing with order of input .

- if your inputs are other than GeneIDs (such as refseq IDs) you'll have to write some variation on the above.

 

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Malcolm.Cook1.0k

What if I have to do this by using R in windows? The mouse Ids are gene identifiers from Illumina platform.

ADD REPLYlink written 3.7 years ago by Bioinformatist Newbie230
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