<p>Hi An Ignorant Wanderer,</p>
<p>Yes, you're right - ENST00000414213 is a deprecated ID from Ensembl release 75.</p>
<p><a href="https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213" rel="nofollow noreferrer">https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213</a></p>
<p>To convert a list of IDs from GRCh37, you will need to use the GRCh37 dataset. You can do this using the following documentation/example:
<a href="https://www.ensembl.org/info/data/biomart/biomart_r_package.html" rel="nofollow noreferrer">https://www.ensembl.org/info/data/biomart/biomart_r_package.html</a></p>

CC BY-SA 4.0
2022-11-09T12:09:51.040Z
2022-11-09T12:09:51.040Z
Ben_Moore
<p>When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs:</p>
<pre><code>mart &lt;- useMart(&quot;ensembl&quot;, dataset = &quot;hsapiens_gene_ensembl&quot;)
ensemble2gene &lt;- getBM(attributes=c(&quot;ensembl_transcript_id&quot;, 
                                    &quot;external_gene_name&quot;,
                                    &quot;ensembl_gene_id&quot;),
                       filters = &quot;ensembl_transcript_id&quot;,
                       values = as.list(transcripts), 
                       mart = mart)
</code></pre>
<p>some of rows returned have NA values for both the gene name and Ensembl gene ID. This is a bit odd because for example, one of the transcript IDs with missing gene IDs is ENST00000414213 but when I google it, I find that it corresponds to gene ENSG00000235143 (according to <a href="http://genome-euro.ucsc.edu/cgi-bin/hgGene?hgg_gene=ENST00000431202.1&amp;hgg_chrom=chr1&amp;hgg_start=30858157&amp;hgg_end=30860254&amp;hgg_type=knownGene&amp;db=hg38" rel="nofollow noreferrer">this</a>). Why am I getting missing results in <code>getBM</code> then? Is it because maybe the transcript is from an old version of the database? If so, is that the only reason or are there other reasons this could be happening?</p>

<r><ensembl><biomart>
Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?
# Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

(Asked by: username_0 on 2022-11-05)

When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs:
mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
ensemble2gene <- getBM(attributes=c("ensembl_transcript_id", 
                                    "external_gene_name",
                                    "ensembl_gene_id"),
                       filters = "ensembl_transcript_id",
                       values = as.list(transcripts), 
                       mart = mart)

some of rows returned have NA values for both the gene name and Ensembl gene ID. This is a bit odd because for example, one of the transcript IDs with missing gene IDs is ENST00000414213 but when I google it, I find that it corresponds to gene ENSG00000235143 (according to this). Why am I getting missing results in getBM then? Is it because maybe the transcript is from an old version of the database? If so, is that the only reason or are there other reasons this could be happening?

**Tags:** r, ensembl, biomart

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## 1 answers

### Answer by username_1 on 2022-11-09. Score: 0 | Accepted answer

Hi An Ignorant Wanderer,

Yes, you're right - ENST00000414213 is a deprecated ID from Ensembl release 75.

<https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213>

To convert a list of IDs from GRCh37, you will need to use the GRCh37 dataset. You can do this using the following documentation/example:
<https://www.ensembl.org/info/data/biomart/biomart_r_package.html>


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