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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?
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  • $\begingroup$ 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. $\endgroup$
    – Community Bot
    Commented Mar 5, 2023 at 13:00
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    $\begingroup$ 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. 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. $\endgroup$
    – gringer
    Commented Mar 5, 2023 at 16:23

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