Volcano plots and heat maps showing the time course of acoustic trauma-related differential gene expression in the zebrafish inner ear. RNA samples from zebrafish inner ears of controls or subjects exposed to acoustic trauma and allowed to recover for either two or four days and then hybridized to a zebrafish microarray, which measures expression (mRNA abundance) for 21,000 gene transcipts. Volcano plots show differential gene expression between (A) controls and two days post-trauma (D2), (B) controls and four days post-trauma (D4), and (C) two versus four days post-trauma. The Y-axes of the volcano plots display the negative log (base 10) of P values from paired t-tests, while the X-axes show the log (base 2) of the fold differences between the groups. The horizontal line represents the P = 0.05 value, and the vertical lines corresponding to fold differences of 1.4 and -1.4, respectively. Genes with paired t-test P < 0.05, and fold difference ≥ 14 or ≤-1.4, were identified as differentially expressed genes and lie outside the lines (in red). (D) The heat map shows the level of expression (red: greater up-regulation, blue: greater down-regulation) of each of these genes in all six samples (column 1-3: controls, column 4-6: Day 2, column 6-9: Day 4). An enlargement of the heatmap to the right shows that distinct patterns of gene expression were evident for each of these three datasets.
Schuck et al. BMC Neuroscience 2011 12:88 doi:10.1186/1471-2202-12-88