<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>

CC BY-SA 4.0
2022-09-23T08:17:59.757Z
I tried putting a bunch of entrez id genes and I got nothing useful it seems? https://imgur.com/tZc6Vk8.png
gl00ten
CC BY-SA 4.0
2022-09-21T06:40:30.057Z
2022-09-21T06:50:23.553Z
2022-09-21T06:50:23.553Z
Nitesh Shriwash
<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>

<gene><gene-ontology><ontology>
Building a group representation of genes' ontologies
# 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

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## 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  

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