Correlated gene clusters. (A) Representation of the voxelation process on a normal hemisection. Abbreviations: Ca, tail of caudate nucleus; Cx, cortex; Hi, hippocampus; Pu/GP, putamen/globus pallidus; Th, thalamus. (B) Gene expression correlation matrices for the normal and Alzheimer's hemisections. The correlation of expression levels across voxels between any two genes is read by looking along the relevant row and column, and finding the intersection. The darkness of the corresponding element gives the correlation between that pair of genes by reference to the scales (right). The diagonals are the autocorrelations of the gene expression patterns for each gene and are (and should be) equal to one. All other correlations must be between 1 and −1. The genes are parsimoniously ordered in the normal correlation matrix, giving five clusters. The order of genes in the Alzheimer's matrix follows the normal. (C) Gene expression correlation matrices for the subset of genes common to both specimens that display a spatial expression correlation coefficient of >0.92 with at least one other gene within the same brain. The genes in the normal correlation matrix are ordered using a similarity metric, and the order of genes in the Alzheimer's matrix is the same as for the normal. Two mutually exclusive clusters of coregulated genes are present: cluster 1 (genes 1–14) and cluster 2 (genes 15–46). In both (B) and (C), the similarity of the correlation matrices between the two specimens is highly significant, as judged using a Monte-Carlo simulation. (D) Spatial gene expression patterns for the subset of correlated genes. The voxels are laid out in linear fashion forming the columns of the matrices, whereas the genes form the rows. The relative level of expression of a gene in any particular voxel can be deduced by reference to the scales below. The two clusters of genes are apparent, and although each cluster consists of highly correlated expression patterns within both the normal and Alzheimer's hemisections, the patterns of gene expression are different between the two hemisections.
