Figure 3. Scatter plots showing distribution of Cy5 signal intensity (noise-exposed cochlea) versus Cy3 signal intensity (control cochlea) at each of the 8750 grid locations on the microarray. Signal intensities ranged from 30 to 20,000 with most values falling between 50 and 5000. Top panel compares Cy5 labelling after 3 h of noise exposure with Cy3 labelling in control cochleae; bottom panel shows similar comparison, but after 6 h of noise exposure. Diagonal line, labelled 1, in upper right corner of each panel represents a Cy5/Cy3 ratio of 1, i.e., gene expression in the noise-exposed cochlea was the same as in control cochlea. Diagonal line of –2 indicates that the signal intensity in the noise-exposed ears (Cy5) was twice as great as that in the control ears (Cy3). Diagonal line of +2 indicates that the signal intensity in the noise-exposed ears (Cy5) was half as great as in the control ears (Cy3). For the 3-h exposure (top panel), most signal values are clustered along the diagonal between –1.5 and +1.5 indicating similar levels of gene expression in normal and noise-exposed cochlea. For the 6-h exposure (bottom panel), a large cluster of points can be seen above the –2-labeled diagonal line near the lowerleft portion of the panel, i.e., these gene transcripts show more than a two-fold increase in expression after the 6-h exposure compared to the control cochlea.