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Significant fold changes were judged considering the following criteria: statistical significance of individual ΔCt values at P <0.01 and biological significance at fold change ≥2.
The number of genes manifesting significant fold changes (/fold ratio/> 2) was greater in layer 1 and 4 groups than in layer 2 and 3 groups.
A significant fold change was based on controlling the false discovery rate (FDR) at less than 5.
Significant fold change values (p-value<0.05) are indicated by asterisks at the top of the figure.
The P-value cutoff was set to 0.01, a Benjamini-Hochberg correction was applied and the significant fold difference was considered two-fold above or below baseline.
The absence of significant fold changes in activated microglial markers in particular argues against a substantial glial component to neurodegeneration in the terminal PD brain.
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To evaluate proteins that showed significant fold-changes between the co-culture and monoculture systems, an empirical Bayes moderated t test was performed.
This selection was based on the fact that these miRNAs produced the most significant fold-changes in our study.
All five genes showed significant fold-changes in a direction concordant to that as observed in the microarray, confirming the validity of the results (Figure 2).
However, even after applying these filters, many redundant probe sets showed significant fold-change differences relative to each other, suggesting differential regulation of alternative transcript production.
Significant fold-changes (p ≤ 0.01) indicated indicated in bold.
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