Volcano plots are a convenient way of visualizing RNA-seq data. The x-axis is a measurement of biological effect of a variable (time, genotype or the interaction between them). The y-axis is a measurement of the probability that a deviation from the mean as extreme or more than the observed value happens given that the null hypothesis is true. In practice, we are often interested in the genes that have the lowest q-value and the largest effect size.
In the plots below, green points are genes that are not transcription factors, and orange points are transcription factors.