<p><div><div><div><div data-width="100" data-show-faces="false" data-send="true" data-layout="button_count" data-height="21" data-href="https://www.r-bloggers.com/converting-mouse-to-human-gene-names-with-biomart-package/"></div></div><div><a data-url="https://www.r-bloggers.com/converting-mouse-to-human-gene-names-with-biomart-package/" data-counturl="https://www.r-bloggers.com/converting-mouse-to-human-gene-names-with-biomart-package/" data-count="horizontal" data-text="Converting mouse to human gene names with biomaRt package" class="twitter-share-button" data-via="rbloggers" href="https://twitter.com/share"></a></div><div></div></div><div></div></div>
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(This article was first published on <strong><a href="https://rjbioinformatics.com/2016/10/14/converting-mouse-to-human-gene-names-with-biomart-package/"> Let's talk about science with R</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p>Converting mouse gene names to the human equivalent and vice versa is not always as straightforward as it seems, so I wrote a function to simplify the task. The function takes advantage of the <strong>getLDS()</strong> function from the <strong>biomaRt</strong> to get the hgnc symbol equivalent from the mgi symbol. For example, let’s convert the following mouse gene symbols, <em>Hmmr</em>, <em>Tlx3</em>, and <em>Cpeb4</em>, to their human equivalent.</p>
<pre>
musGenes &lt;- c(&quot;Hmmr&quot;, &quot;Tlx3&quot;, &quot;Cpeb4&quot;)

# Basic function to convert mouse to human gene names
convertMouseGeneList &lt;- function(x){

require(&quot;biomaRt&quot;)
human = useMart(&quot;ensembl&quot;, dataset = &quot;hsapiens_gene_ensembl&quot;)
mouse = useMart(&quot;ensembl&quot;, dataset = &quot;mmusculus_gene_ensembl&quot;)

genesV2 = getLDS(attributes = c(&quot;mgi_symbol&quot;), filters = &quot;mgi_symbol&quot;, values = x , mart = mouse, attributesL = c(&quot;hgnc_symbol&quot;), martL = human, uniqueRows=T)
humanx &lt;- unique(genesV2[, 2])

# Print the first 6 genes found to the screen
print(head(humanx))
return(humanx)
}
</pre>
<p>We can just as easily write a function to go from human to mouse genes.</p>
<pre>
# Basic function to convert human to mouse gene names
convertHumanGeneList &lt;- function(x){

require(&quot;biomaRt&quot;)
human = useMart(&quot;ensembl&quot;, dataset = &quot;hsapiens_gene_ensembl&quot;)
mouse = useMart(&quot;ensembl&quot;, dataset = &quot;mmusculus_gene_ensembl&quot;)

genesV2 = getLDS(attributes = c(&quot;hgnc_symbol&quot;), filters = &quot;hgnc_symbol&quot;, values = x , mart = human, attributesL = c(&quot;mgi_symbol&quot;), martL = mouse, uniqueRows=T)

humanx &lt;- unique(genesV2[, 2])

# Print the first 6 genes found to the screen
print(head(humanx))
return(humanx)
}

genes &lt;- convertMouseGeneList(humGenes)
</pre>
<p>If you have any other suggestions on how to convert mouse to human gene names in R, I would love to hear them just email me at info@rjbioinformatics.com.</p>
<p> </p>
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