Most genes showing increased expression with Braak stage are confirmed with qRT-PCR. (a) Box plots showing expression levels (y-axis) for five of the top genes differentially expressed with Braak stage in control (x-axis). P-values of differential expression were measured using a t-test (**, P < 0.003; ***, P < 0.0004). (b) Fold changes (y-axis) for each of these genes between Braak stages of 1 and 2 were calculated using three methods (x-axis): microarray (M), qRT-PCR of tissue from hippocampus (HP), and qRT-PCR of tissue from frontal cortex (C). Genes were rated as confirmed (tick; fold change >1.2), marginal (minus sign; 1.1 < fold change < 1.2), and non-confirmed (cross; fold change <1.1).