Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates

Selinger, Christian; Tisoncik-Go, Jennifer; Menachery, Vineet D; Agnihothram, Sudhakar; Law, G Lynn; Chang, Jean; Kelly, Sara M; Sova, Pavel; Baric, Ralph S; Katze, Michael G

Functional analysis of statistically significant gene expression changes was performed using Ingenuity Pathways Knowledge Base (IPA; Ingenuity Systems). For all gene set enrichment analyses, a right-tailed Fisher's exact test was used to calculate P-values associated with each biological function and canonical pathway. Upstream Regulator Analysis in IPA was used to predict regulators and infer their activation state based on prior knowledge of expected effects between regulators and their known target genes according to the Ingenuity Knowledge Base (IKB). The calculated z-score signifies whether gene expression changes for known targets of each regulator are consistent with what is expected from the literature (z > 2, regulator predicted to be activated, z < -2, regulator predicted to inhibited). In addition to IPA Upstream Regulator Analysis, we also used EnrichR [46] , a collaborative gene list enrichment tool, to determine possible upstream regulators via overrepresented transcription factor binding site motifs [47] . Causal Network Analysis in IPA was used to understand gene expression changes and causal relationships between genes and networks of upstream regulators in the experimental dataset. The genes within the causal network represent nodes and the edge that defines the biological relationship between two nodes is represented as an arrow signifying regulation. Dashed arrows represent indirect relationships and solid arrows represent direct relationships. All edges are supported by at least one published reference or from canonical information stored in IKB.