Functional annotation analysis. Significantly over-represented GO annotations were detected among the 115 changed genes (206 exon probesets). Only GO annotations with at least 3 genes and P < 0.01 (Fisher exact probability) are presented here. The complete data of enriched GO annotations with P < 0.05 and a threshold of 2 genes are available in Additional file 3, Table S2. For each annotation, the dark bar represents the number of observed genes among the differentially expressed genes, and the grey bar represents the number of expected genes among the core-level Human Exon 1.0 ST Array.

Confirmation of the differential expression of B cell-related genes. Quantitative Real-Time RT-PCR analyses were performed to confirm the expression changes in CD19, CD22, CD79A, IGHD, IGHM and PAX5 genes (A-F). SNCA gene expression was used as a negative control (G). Each transcript's expression level was normalized to the geometric mean of GUSB and TBP expression levels (H). Graphs in column I (AI-HI, Two-way ANOVA, followed by Tukey post hoc) represent the combined analysis of men and women (79 samples). Each analysis included a group of sex- and age-matched healthy controls, and three groups of patients: PD-patients that did not receive anti-Parkinson medications at time of enrollment (naïve-PD), PD-patients with short disease duration (PD-SDD) and PD-patients with long disease duration (PD-LDD). Each of these four groups included both women and men in a 1:1 ratio. Graphs in columns II and III (AII-HII and AIII-HIII, One-way ANOVA, followed by Tukey post hoc) represent the separate analysis of women (40 samples) or men (39 samples), respectively. For all gene analyses, bold numbers in AI-AIII represent the number of individuals tested. Bars represent mean ± SEM. Significant P-values are indicated between the tested groups as follows: black solid lines represent P < 0.0005, black dashed lines represent P < 0.005 and grey solid lines represent P < 0.05. Statistical significances were detected (Two-way ANOVA) for both gender and group parameters (#) and for gender and group parameters, as well as the interaction between them (*).

Significant expression changes in peripheral blood leukocytes of Parkinson's disease patients compared to controls. (A) Schematic representation of the statistical analysis and the filters applied on the Affymetrix GeneChip Human Exon 1.0 ST Array exon-level expression data. The numbers of exon-level probesets remained after each filtering step are indicated in circles. (B) PCA mapping of patients and control samples according to the expression levels of the 206 significantly changed exon probesets.

B cell-related genes in the network of differentially expressed genes. The Pearson Correlation test between the expression levels of the 115 differentially changed genes generated two gene networks. Highly significant correlations with a threshold of r > 0.8 and P < 10^-14 are presented here. B cell-related genes are in bold circles. Complete correlation data are available in Additional file 5, Table S4.