KO differential predictions using DESeq2

[L F]

Hello,

I am a beginner in the use of this tool. I have a question concerning the results obtained from picrust2 on which I applied a test to know the KOs that are differentially expressed according to the location of my samples. It turns out that I have 3 KOs overexpressed in location B, against 7 in location A. My question is that I am not sure I understood the interpretation. For example, in the 3 KOs detected there is K16922. Searching for which pathway they belong to I found "yydH; putative peptide zinc metalloprotease protein". This is not a pathway... so I don't know how to interpret this. If you can help me

[Gavin Douglas]

Hi there,

So it looks like that’s the gene matching that KEGG ortholog, which is a lower level whereas the pathways are higher groupings. You can look into how KEGG orthologs are defined (which are a type of “gene family” made up of many genes - many of which apparently can be described as a putative peptide zinc metalloprotease protein.

Hopefully that makes sense!

Cheers,

Gavin

On May 16, 2022, at 5:21 AM, L F <bbi...@gmail.com> wrote:

Hello,

I am a beginner in the use of this tool. I have a question concerning the results obtained from picrust2 on which I applied a test to know the KOs that are differentially expressed according to the location of my samples. It turns out that I have 3 KOs overexpressed in location B, against 7 in location A. My question is that I am not sure I understood the interpretation. For example, in the 3 KOs detected there is K16922. Searching for which pathway they belong to I found "yydH; putative peptide zinc metalloprotease protein". This is not a pathway... so I don't know how to interpret this. If you can help me

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[L F]

Hi Gavin,

First thank you for your answer. So if I undeserstood, it means that this gene family is more represented in location B than A? what disturbs me is that I would have liked to see in which pathways it can be impacted (especially in the rodent because it is the subject of my study), if it's possible (I've checked the metacyc pathways but based on the parameters we choose in DESeq2 they're not significative, only for the KO)

[L F]

For example, I have a bunch of type III secretion protein detected in location A, so that means that individuals living there expressed these protein more thant the one living in location .... Sorry, just trying to understand ^^

[Gavin Douglas]

Hi there,

Yes that is the interpretation of the test. It’s important to appreciate that depending on what differential abundance test you apply that you can get different results though (e.g., https://www.nature.com/articles/s41467-022-28034-z). Also, it’s important to clarify that the organisms in location A are *predicted* to have more type III secretion proteins. Since this is based on the 16S only, this comes with major caveats.

Hopefully that helps!

Gavin

To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/621dd0ab-4593-4808-8104-2103bb1a9d07n%40googlegroups.com.

[L F]

Thank you very much !!! It helped me a lot :)