Nearly all volcano plot I've seen tend to be roughly symmetric around the y-axis, with a fairly equal number of up- and down-regulated genes. What are the potential reasons for a volcano plot that is heavily unbalanced (i.e., many more negative fold change genes than positive)?
In my analysis, I have identified two populations of patients within a disease cohort, representing the "interferon high" and "interferon low" sub-populations. I then calculate differential expression between these groups, and visualize the results with a volcano plot (log(p-value) of differential expression vs. log(fold change)). The volcano plot is quite asymmetric, with a maximum log2 fold change of 1 on the positive end, and a minimum log2 fold change of -3 on the negative end, with many more genes significantly down-regulated in the IFN-low population.
Is it reasonable to suppose that there are lots of genes up-regulated in IFN-high, with no down-regulated genes defining this population, or is there something else going on?