Figure 4.

Spatial gene expression patterns for the subset of correlated genes. (A) Spatial expression patterns of the genes shown in Figure 3D for the normal and MA brains. The relative level of expression of any gene in any voxel is read by looking along the relevant row and column, finding the intersection, and referring to the scales. The voxel numbering in the columns of the matrix is such that voxels A1, A2, A3, …, I2, I3, I4 correspond to voxels 1, 2, 3, …, 37, 38, 39, 40, respectively. The genes are in the same order as for Figure 3D. The two clusters of genes are apparent, and although these have highly conserved patterns of expression within the normal and PD brains, these patterns are somewhat divergent between the two brains. (B) Level of TH expression as judged using real-time QRT-PCR. TH expression levels are found to peak in voxels corresponding to the olfactory bulb (A1–A4, voxels 1–4) and the substantia nigra (G3, G4, corresponding to voxels 27, 28; and H3, H4 corresponding to voxels 31, 32). However, the level of TH in the substantia nigra of the PD brain is substantially decreased compared with the normal brain (Fig. 1D). (C) The Nfl gene is present as two separate spots on the microarrays, corresponding to genes 39 and 50 in A. This provided an opportunity to assess within-array replicability, which was excellent (for the normal brain, r = 0.96, F_[1,38] = 443.65, p < 0.0001; for MA brain, r = 0.90, F_[1,38] = 153.80, p < 0.0001). (D) Expression pattern of the precerebellin-1 gene in the normal and PD brain. The line drawing shows the anatomy of the midlevel transverse section employed, which corresponds to section 8 of the Mouse Brain Library (interaural 5.40 mm, bregma −4.60 mm). (Olf) Olfactory lobes; (Str) striatum; (Hi) hippocampus; (Ce) cerebellum. Imaging software smoothed the expression patterns over the voxels. Gene expression levels can be deduced by reference to the pseudocolor scales.