Answers.Body: <p>Have you tried <a href="https://david.ncifcrf.gov/summary.jsp" rel="nofollow noreferrer">DAVID</a> for functional annotation (Gene Ontology and KEGG terms)?</p>
  <p>I usually use DAVID to extract GO and KEGG terms and plot the results using R.</p>
  <p>If you also want to plot a protein-protein interaction (PPI) network for your gene list you can use STRING database to extract interactions and network and use Cytoscape for visualizing this result.</p>
  
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Answers.CreationDate: 2022-09-23T08:17:59.757Z
Answers.Text: I tried putting a bunch of entrez id genes and I got nothing useful it seems? https://imgur.com/tZc6Vk8.png
Answers.UserDisplayName: gl00ten
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-09-21T06:40:30.057Z
Answers.LastActivityDate: 2022-09-21T06:50:23.553Z
Answers.LastEditDate: 2022-09-21T06:50:23.553Z
Answers.UserDisplayName: Nitesh Shriwash
Body: <p>I have a list of genes (about 2000) from lines of <strong>drosophila subobscura</strong>, in the following format:</p>
  <ul>
  <li>LOC117900589</li>
  <li>LOC11788959</li>
  <li>LOC11790331</li>
  </ul>
  <p>I'm trying to represent this set of genes in a useful way.</p>
  <p>So, I was recommended to represent the ontology function of these genes in a graphical way.
  I was recommended this tool:
  <a href="http://cbl-gorilla.cs.technion.ac.il/" rel="nofollow noreferrer">http://cbl-gorilla.cs.technion.ac.il/</a></p>
  <p>One inputs a list of genes and it outputs this kind of graph:
  <a href="https://i.sstatic.net/cQZXm.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cQZXm.png" alt="GOrilla example output" /></a></p>
  <p>The problem is that, this tool, GOrilla only accepts genes from <strong>drosophila melanogaster</strong>.</p>
  <p>I have to either:</p>
  <ul>
  <li><strong>a)</strong> convert the genes id to a homologous gene in <strong>melanogaster</strong></li>
  <li><strong>b)</strong> find an alternative tool</li>
  </ul>
  <p>A solution to either a) or b) would be helpful. Or an alternative solution.</p>
  <p>For a) I tried:</p>
  <ul>
  <li>Ncbi's <strong>homologene</strong>: which doesn't seem to be working for a the genes ID I tried so far (I didn't try them all)</li>
  <li>Blasting the gene sequence on melanogaster's genome and looking through the list manually to find an homologous gene.</li>
  </ul>
  <p>So far these methods have been impractical for the number of genes I have.</p>
  
Tags: <gene><gene-ontology><ontology>
Title: Building a group representation of genes' ontologies
ThreadText: # Building a group representation of genes' ontologies
  
  (Asked by: username_0 on 2022-09-15)
  
  I have a list of genes (about 2000) from lines of **drosophila subobscura**, in the following format:
  
  * LOC117900589
  * LOC11788959
  * LOC11790331
  
  I'm trying to represent this set of genes in a useful way.
  
  So, I was recommended to represent the ontology function of these genes in a graphical way.
  I was recommended this tool:
  <http://cbl-gorilla.cs.technion.ac.il/>
  
  One inputs a list of genes and it outputs this kind of graph:
  [![GOrilla example output](https://i.sstatic.net/cQZXm.png)](https://i.sstatic.net/cQZXm.png)
  
  The problem is that, this tool, GOrilla only accepts genes from **drosophila melanogaster**.
  
  I have to either:
  
  * **a)** convert the genes id to a homologous gene in **melanogaster**
  * **b)** find an alternative tool
  
  A solution to either a) or b) would be helpful. Or an alternative solution.
  
  For a) I tried:
  
  * Ncbi's **homologene**: which doesn't seem to be working for a the genes ID I tried so far (I didn't try them all)
  * Blasting the gene sequence on melanogaster's genome and looking through the list manually to find an homologous gene.
  
  So far these methods have been impractical for the number of genes I have.
  
  **Tags:** gene, gene-ontology, ontology
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-09-21. Score: 1
  
  Have you tried [DAVID](https://david.ncifcrf.gov/summary.jsp) for functional annotation (Gene Ontology and KEGG terms)?
  
  I usually use DAVID to extract GO and KEGG terms and plot the results using R.
  
  If you also want to plot a protein-protein interaction (PPI) network for your gene list you can use STRING database to extract interactions and network and use Cytoscape for visualizing this result.
  
  > **Comments:**
  > **username_0**: I tried putting a bunch of entrez id genes and I got nothing useful it seems? https://imgur.com/tZc6Vk8.png  
  
  ---
  
  