Fig. 5.

Transcriptomic analyses of rotenone effect on Kyoto of Encyclopedia of Genes and Genomes (KEGG) pathways. (A) Venn diagram of differentially expressed genes after 5 μM rotenone treatment of 2, 4 and 8 weeks BrainSpheres. The number of genes altered by chemical treatment increased over time and profiles were more similar between 4 and 8 weeks, than when compared to 2 weeks. (B) Heatmap of median rank for the significant KEGG pathways. The analysis was performed after exposure of 2, 4 and 8 weeks differentiated BrainSpheres to rotenone. The pattern at 2 weeks was more different than what was observed at 4 and 8 weeks. (C) shows the direction of the overall change for the significant pathways at the three time-points. There was only one up-regulated pathway (p53 signaling pathway shown in orange) and the rest corresponded to down-regulated pathways (shown in blue). (D) Bubble plots of the significance of the KEGG pathways at 2 weeks (D1), 4 weeks (D2) and 8 weeks (D3). The upper right corners of the plots contain bubbles corresponding to pathways with a strong directional change and high −log₁₀ p-value. All the significant pathways were down-regulated (colored in blue), expect the p53 signaling pathway (hsa04115) in D1. (E) shows real-time qPCR validation for six genes found to be altered by microarrays, including NR4A2 (E2), LHX1 (E3) and DCX (E5). Results represent mean ± SD (n = 3). Asterisks indicate p-values from two-way ANOVA multiple comparison (p < 0.01 = *; p < 0.001 = **; p < 0.0001 = ***). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)