Analyzing upstream regulators can clarify the pathway findings by looking for commonalities in their regulation, i.e. it may be possible to identify sets of differentially expressed genes that are downstream targets of specific transcription factors, cytokines, signaling cascades, and endogenous and exogenous chemicals. Both the glucocorticoid and aldosterone pathways were significantly altered in alcoholic brains, and the upstream effectors analysis indicated that their receptors, NR3C1 and NR3C2, are in an activated state (Supplemental Table S3). Other genes identified as activated include many regulators related to immune function (including cytokines IL1B, IL10, IL11, IL15, IL17A, and EDN1), other regulators, including hypoxia-related gene HIF1A and Endothelial PAS domain-containing protein 1 (EPAS1), and 2 genes that are general indicators of stress, TP53 and TGFB1. The expression of downstream targets for the Wnt/β catenin pathway and the ERBB4 pathways involved in neurogenesis (Lazarov & Marr, 2010), including TCF4 and cyclin D1, provide evidence that both of these pathways were less active in the alcoholics (Supplemental Table S3).
