Genetic, Transcriptome, Proteomic, and Epidemiological Evidence for Blood-Brain Barrier Disruption and Polymicrobial Brain Invasion as Determinant Factors in Alzheimer’s Disease

Carter, Chris J.

Assuming a human genome of 26846 coding genes and an interactome or other gene set of N genes one would expect N/26846 to exist in the comparator dataset. For example, when comparing 2879 misregulated AD hippocampal genes against any pathogen interactome one would expect 2879/26846 (10.7%) to figure in the pathogen interactome. This calculation was used to define expected values and the enrichment values (observed/expected) in relation to other datasets. Significance of the enrichment was calculated using the hypergeometric probability test. The resultant p values from each analysis series were corrected for false discovery (FDR) [110] . Nominally significant FDR corrected values are considered at p < 0.05 and a corrected Bonferroni p value threshold is illustrated on each set of graphs. (Bonferroni P = 0.05/N, where N is the maximum number of possible comparisons for each situation (e.g., 78 AD genes or 1690 upregulated genes in the AD hippocampus).