I'm using GEO2R in order to identify the DEGs, I set the significance level cut-off as 0.05. After the analysis, the log2 fc threshold was set automatically around 0.2 and 419 genes were defined as significant degs based on this threshold.
My question is; can we consider genes with such fold change as significant degs?
There is no prescribed logFC that everyone follows. The point is to convince yourself and others - those reviewing your papers and grants - that a particular fold change is meaningful. In my experience, most people will not argue with logFC =>1, but you may get pushback for smaller numbers.
You will probably hear other opinions from people who look at it primarily from a statistical point of view. They might say that a combination of logFC and p-values could be significant even when logFC <=0.5, but I don't know (m)any biologists who readily subscribe to that idea.
Given that you have 419 candidates at 0.2, I suspect you would still have a healthy number after raising logFC to 1. If some genes with logFC <1 fit the narrative of other genes with logFC =>1, you can always bring them into the story while recognizing that their expression is below the threshold.