Fold change, p-value and FDR for treatment were imported into Ingenuity Pathway Analysis Fall, September 2018 release (IPA; QIAGEN Inc.). For comparisons of alcohol treated vs. untreated cells, pathway and upstream regulator analyses were carried out on genes with FDR< 0.05 and absolute fold ≥ 1.2, a total of 2318 genes, to keep the number within the 3000 limit suggested by the software vendor. For untreated cells from AD vs. control subjects, 465 genes with p < 0.05 and absolute fold ≥ 1.2 were compared; although the low stringency means that false positives will be included in the analysis, random noise should not greatly affect the results since pathways are tested for significance above random sets of genes. Upstream analysis identifies possible upstream regulators that could produce parts of the pattern of results seen in the data. Upstream regulators with absolute z-score ≥ 1.9 were considered to be likely causes of the pattern of gene expression changes.
