During an RNA-Seq study on a plant, we observe that most differentially expressed genes are down-regulated. The upregulated genes relate to defense pathways, while the downregulated ones relate to more day-to-day processes, such as growth. Is this distribution of downregulated and upregulated genes normal?
I also know that the numbers of downregulated pathways and upregulated pathways are more similar. My explanation is that day-to-day processes are more redundant and finely regulated, so downregulating them necessitates to change the expression of more genes than those in more point-in-time, strong-hitting pathways. Have you observed something similar?