Pathway issue

[SimonE1220]

Hey, sorry for bothering you with more issues.
I have an error with the pathway analysis could you please help me.
I am running seaborn 0.11.2 on Python 3.10.11

[earmingol]

Unfortunately KEGG is not available for mouse, only 'GOBP' and 'Reactome' works with mouse. 'KEGG' is available only for human at the moment.

We will eventually add KEGG for mouse.

[SimonE1220]

Thank you, worked now.

[dbdimitrov]

Hi @SimonE1220,

Great to hear that it worked. Just in case you want to use other resources, you could check this vignette for resource orthology conversion: https://decoupler-py.readthedocs.io/en/latest/notebooks/translate.html

[SimonE1220]

Thanks a lot for your response. I have one more question intepreting the results. For example i have condition A and B. And than i perform the progeny analsis, it shows that Nfkb activity is upregulated wheras Jak-Stat activity is reduced. How do I know if the activity is upregulated in condition A or B, so whats the reference ?
Thank you very much.

[dbdimitrov]

Hi @SimonE1220,

High interaction loadings (and hence pathway activities estimated on those) should be linearly associated with your sample/context loadings.

So, whichever A or B has high loadings in your factor of interest is also the condition where NFKB activity is up. The same goes for JAK-STAT - i.e. it's down in the samples with high loadings.

For the samples with low loadings, you can think of the pattern (i.e. signaling captured by Factor X) as not being strongly associated with those.

Hope this helps!

[SimonE1220]

@dbdimitrov
Thanks a lot that realy helps me.