Network analysis and comparison of regulation in H1299 shRAD9 cells directly irradiated and corresponding to bystander positive (DBP) or to bystander negative (DBN) cells. A. Venn diagram of overlap in significantly differentially expressed genes from directly irradiated cells corresponding to bystander positive, DBP and those corresponding to bystander negative, DBN cells, constructed using VENNY. Venn diagrams were generated using Venny . B. Ingenuity Pathways analysis (IPA) generated HIF1α network connecting to genes that were only significantly changed in DBP cells, left of the HIF1α node, and genes that were only significantly changed in DBN cells, right of HIF1α node. In the upper panel, genes are overlaid with relative expression levels in directly irradiated cells corresponding to bystander positive (DBP). In the lower panel, genes are overlaid with relative expression in directly irradiated cells corresponding to bystander negative (DBN). Up regulated genes are red and down regulated genes green, with fold changes shown under the nodes. Blank nodes are genes that were in network but not in the dataset used to show fold-changes. Solid edges (lines and arrows between nodes) depict direct interactions between molecules and dashed lines represent indirect associations between molecules based on information in the Ingenuity knowledge base. Orange colored lines and nodes represent known activation and blue colored lines and nodes represent known inhibition. A grey line represents an unchanged or unpredicted relationship between two nodes.