Figure 3.

Evaluating mRNA expression neighborhoods for enrichment in mitochondrial genes. (A) Schematic illustration of the mitochondria neighborhood index. The coordinate of each gene (circle) is defined by its expression vector in an mRNA microarray experiment. Genes are close to one another if they have similar expression profiles (based on an appropriate distance metric, see Methods). The mitochondria neighborhood index, N_R(G), is defined as the number of known mitochondrial genes (orange circles) among the R nearest neighbors of the query gene, G (blue circle). In this cartoon, N₁₀ = 5 because there are five mitochondrial genes within the query's 10 nearest-neighboring genes. (B) Distribution of N₁₀₀ values. The blue histogram shows the distribution of N₁₀₀ for all genes, and the red histogram plots N₁₀₀ for known mitochondrial genes, in expression set 4. *, the histogram bin containing LRPPRC (see text and Table 1).