<p>I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the transcriptome, I ran eggnog-mapper annotation.</p>
<p>After running eggnog mapper, I extract the list of GO, KEGG and COG terms associated.</p>
<p>From there, I would like to do a Fisher-test to highlight COG categories overrepresented in our querry selected list compared to our reference transcriptome.</p>
<p>My questions:</p>
<ul>
<li>How do you deal with enrichment, this kind of test for COG categories?</li>
<li>For the eggnog results KEGG, EC ...ETC, for example how to assign each KO number to metabolism, • genetic information processing • environmental information processing • cellular processes • organismal systems • human diseases • Drug development
and draw graphs?</li>
</ul>

CC BY-SA 4.0
2023-03-05T13:00:40.250Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2023-03-05T16:23:40.657Z
Hi @se-tima, welcome to Bioinformatics Stack Exchange. The Stack Exchange question / answer approach works best for single specific questions, and not so great for general discussion. If you want a more interactive experience, I recommend you try a discussion website like [reddit](https://reddit.com/r/bioinformatics). Otherwise, please try to limit your post to a single question. If you have multiple questions, feel free to create separate posts for each one.
gringer
<go-enrichment><kegg><eggnog>
COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results
# COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results

(Asked by: username_0 on 2023-03-05)

I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the transcriptome, I ran eggnog-mapper annotation.

After running eggnog mapper, I extract the list of GO, KEGG and COG terms associated.

From there, I would like to do a Fisher-test to highlight COG categories overrepresented in our querry selected list compared to our reference transcriptome.

My questions:

* How do you deal with enrichment, this kind of test for COG categories?
* For the eggnog results KEGG, EC ...ETC, for example how to assign each KO number to metabolism, • genetic information processing • environmental information processing • cellular processes • organismal systems • human diseases • Drug development
  and draw graphs?

**Tags:** go-enrichment, kegg, eggnog
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Hi @se-tima, welcome to Bioinformatics Stack Exchange. The Stack Exchange question / answer approach works best for single specific questions, and not so great for general discussion. If you want a more interactive experience, I recommend you try a discussion website like [reddit](https://reddit.com/r/bioinformatics). Otherwise, please try to limit your post to a single question. If you have multiple questions, feel free to create separate posts for each one.  

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## 0 answers

