Genes with significantly altered expression in the striatum of Pink1−/− mice.

Gene expression was analyzed using NF-κB, PI3 kinase/Akt and cAMP/Ca2+ signaling PCR Arrays (SA Biosciences) as described in the Methods. Ct values (mean ± SD) for individual genes are indicated for wildtype (WT) and Pink1−/− mice. In addition, expression of each gene relative to the housekeeping genes (HKG) is indicated for WT and Pink1−/− mice and was used to calculate the fold change in gene expression (Pink1−/−/WT). All PCR arrays contain five HKG (β-glucuronidase, hypoxanthine guanine phosphoribosyl transferase, heat shock protein 90-alpha, glyceraldehyde-3-phosphate dehydrogenase, and β-actin), to which the expression of the genes of interests is normalized. None of the HKG was differentially expressed between WT and Pink1−/− mice. Data were evaluated and calculated with the ΔΔCt method using the RT2 Profiler PCR Array Data Analysis software and resources available online (http://sabiosciences.com/pcr/arrayanalysis.php). The p values were calculated based on a Student's t-test of the replicate 2−(AVG ΔCt) values for each gene in the WT and Pink1−/− groups. All genes with a pboth genotypes after running five arrays (five mice per genotype were analyzed). Occasionally, a well (gene) yielded no signal at all for reasons that are unrelated to actual lack of expression. For example, if a specific gene became detectable at PCR cycle number 25 in four mice but showed no expression in the fifth mouse of the same genotype, we concluded that this must be an experimental/technical error rather than actual lack of expression and omitted the corresponding data. However, we still used five data points for the other genotype if available. For a description of the function of the listed genes in innate immunity, MAPK signaling and/or their involvement and regulation in PD and models of PD, see the main text and references therein.