Figure 4

Network analysis and comparison of gene regulation in H1299 shRAD9 cells relative to H1299 cells with inherent levels of RAD9. A. Volcano plot showing genes whose expression is significantly altered (blue), when RAD9 is reduced, above the p value cut-off -log₁₀ (0.005) shown as the bold dashed line; log₂ (fold change) on the x-axis and -log₁₀ (p value) on the y-axis. B. Pathways affected after RAD9 reduction in H1299 cells: pathways were ordered by decreasing significance [−log10 (p value)] in down regulated genes (solid grey bars). Up regulated genes (open bars) did not show pathway enrichment. C. Interferon signaling pathway and D. UVA-MAPK signaling pathway were top pathways affected at various levels of signal transduction after RAD9 reduction in H1299 cells. The IPA canonical pathways are shown overlaid with changes of gene expression indicated by different colors. Up regulated genes are red and down regulated genes green, blank nodes are genes that are in the pathway but not in the dataset. Solid lines indicate direct interactions between molecules and dashed lines indicate indirect interactions. Bold grey lines separate cellular compartments, such as extracellular space, cytoplasm, mitochondria and the nucleus. In the UVA-MAPK pathway diagram, signal transduction affects biological processes, such as apoptosis and cell proliferation downstream of nuclear gene expression changes.