Global gene expression network profiles. In 9 V/null lung 391 genes (A) and in 4L lung 345 genes (B) were analyzed as a cascade network using PathwayArchitect 2.0.1 and Ingenuity Pathways Analysis programs. These genes had a high confidence index of direct and indirect interaction with IFNγ/IL-4 macrophage activation genes, which function as core genes (red) and connect to the cascade network via key genes. Gene interactions are shown by the connecting lines. The key genes are those that can be connected to multiple genes. The major key genes are highlighted with different colors for macrophage activation (red), transcription (green), kinase activity (blue), cell death (purple), and signal transduction (yellow) (Additional file 8).