I am using RNA Seq to identify genes that are down-regulated in a mutant cell line for a viral transcription factor compared to WT. The cell line has been infected with a virus and I am specifically interested in viral transcript down regulation.
In the mutant cell line, almost all viral genes are down-regulated although to varying degrees. What would be an acceptable cut off to count as being "down-regulated" in the absence of the factor? Could I use the median of the Log2FC as a cut off or is some other statistic more appropriate?