Figure 4. The use of volcano plots allows for comparison between conditions. Volcano plot displays of genes significantly upregulated and downregulated as a result of different treatments: A: Ciliary neurotrophic factor (CNTF)-based conditions using standard medium (SM) as baseline, (B) fetal bovine serum (FBS)-based conditions using SM as baseline, and (C) CNTF using FBS as baseline (C). With an false discovery rate (FDR) multiple test correction of α<0.05, the p-value cutoff (indicated by red dashed line) was p<.00794424 in (A) and (B), and was p<0.00554170 in (C). The lines drawn at −1 and 1 show the log2 cutoff for significant fold change in A-C. D: Comparison of significantly changed genes for CNTF and FBS treatments, using SM as a control in both cases. The box in (D) is the log2 cutoff for fold change significance. The colors of the data points correspond to the hierarchical cluster analysis in Figure 3 and therefore illustrate the direction of expression changes for genes in those clusters, relative to treatment condition.