Question about pathway analysis

[kiwipeel]

I copy pasted here the bulk data pathway activity tutorial plot. Here we see increase in MAPK pathway in condition 1 compared to condition 2 . Does it mean that this pathways really upregulated (activator genes high) in condition 1 or does it shows genes in this pathway(both supressor and activators) upregulated in condition 1 ?

Also should i use only significantly changed genes in DEGs , or can i use all of the DEGs ?

Thank you;

[PauBadiaM]

Hi @kiwipeel,

Very sorry for the delayed response, somehow I missed your issue!

Regarding your first question, it means that genes with positive weights are being upregulated, while genes with negative weights are being downregulated. You can look at this plot from the python's documentation to get an idea:

Regarding your second question, you should use all DEGs, as enrichment tests (this is an enrichment test) treat genes as observations and the bigger the N the better the estimate.

Hope this is helpful!