Answers.Body: <p>Hugo names don't really have an associated assembly. They are just the official name of the gene in human. You will find them in all assemblies (except if they hadn't been annotated/identified in one of the older ones). Entrez entries are also not tied to a specific genome assembly. They usually have mappings to multiple ones. For example, <a href="https://www.ncbi.nlm.nih.gov/gene/?term=1" rel="nofollow noreferrer">Hugo gene name A1BG, with Entrez ID 1</a> has:</p>
  <p><a href="https://i.sstatic.net/Yj7Wd.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Yj7Wd.png" alt="Screenshot showing the Entrez entry and the hg19 and hg38 coordinates" /></a></p>
  <p>Now, if you want to get Ensembl gene IDs for a list of Hugo gene names, you can use <a href="https://www.ensembl.org/info/data/biomart/index.html" rel="nofollow noreferrer">BioMart</a> to convert. First, get the list of target IDs. You can use either Hugo or Entrez. I found the Entrez simpler to parse out, so I went for those (note that this assumes GNU <code>grep</code>):</p>
  <pre><code>grep -oP '(?&lt;=\()\d+(?=\))' CRISPR_gene_effect.csv &gt; entrez.ids
  
  </code></pre>
  <p>I then went to BioMart and selected &quot;Ensembl genes 104&quot; (note that I could only get Ensembl version 104, I assume you're not adamant about getting version 100 given that it doesn't seem to be current) and &quot;Human genes GRCh38.p13&quot; :</p>
  <p><a href="https://i.sstatic.net/wHKly.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/wHKly.png" alt="BioMart screenshot1" /></a></p>
  <p>Next, I set the filters to &quot;NCBI gene (formerly Entrezgene) ID(s)&quot; and uploaded my file:</p>
  <p><a href="https://i.sstatic.net/DQFII.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/DQFII.png" alt="BioMart screenshot2" /></a></p>
  <p>And, finally, selected the Attributes I want to see, namely Ensembl gene ID, HGNC (Hugo) symbol and Entrez ID so I can map everything to each other:</p>
  <p><a href="https://i.sstatic.net/fykjh.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/fykjh.png" alt="BioMart screenshot3" /></a>
  <a href="https://i.sstatic.net/cJ4vw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cJ4vw.png" alt="BioMart screenshot4" /></a></p>
  <p>I then clicked on &quot;Results&quot; and got:</p>
  <p>[<img src="https://i.sstatic.net/LfrE0.png" alt="BioMart screenshot58" /></p>
  <p>You can now download this to a file and have your mapping. You might even be able to use the one I created: <a href="https://www.ensembl.org/biomart/martview/352aae8e0b5c774cbbee73d67634d577" rel="nofollow noreferrer">https://www.ensembl.org/biomart/martview/352aae8e0b5c774cbbee73d67634d577</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-16T12:54:40.447Z
Answers.Text: Your answer is very helpful. Many thanks!
Answers.UserDisplayName: user345394
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-15T09:00:19.390Z
Answers.LastActivityDate: 2021-10-16T15:36:13.890Z
Answers.LastEditDate: 2021-10-16T15:36:13.890Z
Answers.UserDisplayName: terdon
Body: <p>I want to use a file available on a database called <code>DepMap</code> (<a href="https://depmap.org/portal/download/" rel="nofollow noreferrer">https://depmap.org/portal/download/</a>). This file called <code>CRISPR_gene_effect.csv</code> contains gene ids in the format <code>HUGO (Entrez)</code> eg. <code>TP53 (7157)</code>, without having any complementary information regarding which genome assembly (GRCh37/38) the Entrez ids (and also HUGO symbols) belong to.</p>
  <p>I want to convert these gene ids in the <code>HUGO (Entrez)</code> format to  GRCh38 Ensembl ids (specifically to Ensembl release 100), so that I can map the data to Ensembl's annotations. I would like to get suggestions on this.</p>
  <p>I feel that figuring out the genome assembly version (GRCh37/38) of the Entrez ids would be critical in this conversion. Although, I am not aware if Entrez ids change from one genome assembly to other.</p>
  
Tags: <ensembl><identifiers><entrez>
Title: Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids
ThreadText: # Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids
  
  (Asked by: username_0 on 2021-10-13)
  
  I want to use a file available on a database called `DepMap` (<https://depmap.org/portal/download/>). This file called `CRISPR_gene_effect.csv` contains gene ids in the format `HUGO (Entrez)` eg. `TP53 (7157)`, without having any complementary information regarding which genome assembly (GRCh37/38) the Entrez ids (and also HUGO symbols) belong to.
  
  I want to convert these gene ids in the `HUGO (Entrez)` format to GRCh38 Ensembl ids (specifically to Ensembl release 100), so that I can map the data to Ensembl's annotations. I would like to get suggestions on this.
  
  I feel that figuring out the genome assembly version (GRCh37/38) of the Entrez ids would be critical in this conversion. Although, I am not aware if Entrez ids change from one genome assembly to other.
  
  **Tags:** ensembl, identifiers, entrez
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-10-15. Score: 2 | Accepted answer
  
  Hugo names don't really have an associated assembly. They are just the official name of the gene in human. You will find them in all assemblies (except if they hadn't been annotated/identified in one of the older ones). Entrez entries are also not tied to a specific genome assembly. They usually have mappings to multiple ones. For example, [Hugo gene name A1BG, with Entrez ID 1](https://www.ncbi.nlm.nih.gov/gene/?term=1) has:
  
  [![Screenshot showing the Entrez entry and the hg19 and hg38 coordinates](https://i.sstatic.net/Yj7Wd.png)](https://i.sstatic.net/Yj7Wd.png)
  
  Now, if you want to get Ensembl gene IDs for a list of Hugo gene names, you can use [BioMart](https://www.ensembl.org/info/data/biomart/index.html) to convert. First, get the list of target IDs. You can use either Hugo or Entrez. I found the Entrez simpler to parse out, so I went for those (note that this assumes GNU `grep`):
  
  ```
  grep -oP '(?<=\()\d+(?=\))' CRISPR_gene_effect.csv > entrez.ids
  
  ```
  
  I then went to BioMart and selected "Ensembl genes 104" (note that I could only get Ensembl version 104, I assume you're not adamant about getting version 100 given that it doesn't seem to be current) and "Human genes GRCh38.p13" :
  
  [![BioMart screenshot1](https://i.sstatic.net/wHKly.png)](https://i.sstatic.net/wHKly.png)
  
  Next, I set the filters to "NCBI gene (formerly Entrezgene) ID(s)" and uploaded my file:
  
  [![BioMart screenshot2](https://i.sstatic.net/DQFII.png)](https://i.sstatic.net/DQFII.png)
  
  And, finally, selected the Attributes I want to see, namely Ensembl gene ID, HGNC (Hugo) symbol and Entrez ID so I can map everything to each other:
  
  [![BioMart screenshot3](https://i.sstatic.net/fykjh.png)](https://i.sstatic.net/fykjh.png)
  [![BioMart screenshot4](https://i.sstatic.net/cJ4vw.png)](https://i.sstatic.net/cJ4vw.png)
  
  I then clicked on "Results" and got:
  
  [![BioMart screenshot58](https://i.sstatic.net/LfrE0.png)
  
  You can now download this to a file and have your mapping. You might even be able to use the one I created: <https://www.ensembl.org/biomart/martview/352aae8e0b5c774cbbee73d67634d577>.
  
  > **Comments:**
  > **username_0**: Your answer is very helpful. Many thanks!  
  
  ---
  
  