Maybe this is a trivial question, but I could not find the answer to it yet.

I am analyzing a metatranscriptomics experiment with treatment and control (three replicates each) and I calculated fold changes.

• What does it mean when a gene is upregulated in the treatment? Does this mean that it is downregulated in the control as well or that there is a significant difference in regulation between treatment and control?
• If the second possibility is correct, can I actually find out if the control is downregulated? Or is that only possible if I would have a third condition (treatment-control-null (and how could my null sample look like in this case for a medical analysis)?

If you need additional information, please let me know. Thank you for your help.

"What does it mean when a gene is upregulated in the treatment? Does this mean that it is downregulated in the control as well"

This gets into your particular definition of what baseline "regulation" would look like. Typically the control samples are used to define this.