Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus

Munday, Diane C.; Emmott, Edward; Surtees, Rebecca; Lardeau, Charles-Hugues; Wu, Weining; Duprex, W. Paul; Dove, Brian K.; Barr, John N.; Hiscox, Julian A.

Protein Pathway Analysis-Data were analyzed through the use of Ingenuity Pathways Analysis (Ingenuityா Systems, www.ingenuity. com). Networks were generated using data sets containing gene identifiers and corresponding expression values that were uploaded into the application. Each gene identifier was mapped to its corresponding gene object in the Ingenuity Pathways Knowledge Base. A cutoff of 2.0 was set to identify genes whose expression was significantly differentially regulated. These genes, called focus genes, were overlaid onto a global molecular network developed from information contained in the Ingenuity Pathways Knowledge Base. Networks of these focus genes were then algorithmically generated based on their connectivity. Graphical representations of the molecular relationships between genes/gene products were generated. Genes or gene products are represented as nodes, and the biological relationship between two nodes is repre-sented as an edge (line). All edges are supported by at least one reference from the literature or from canonical information stored in the Ingenuity Pathways Knowledge Base. Human, mouse, and rat orthologs of a gene are stored as separate objects in the Ingenuity Pathways Knowledge Base but are represented as a single node in the network. The intensity of the node color indicates the increased (red) or decreased (green) abundance. Nodes are displayed using various shapes that represent the functional class of the gene product. Canonical pathway analysis utilizes well characterized metabolic and cell signaling pathways that are generated prior to data input and on which identified proteins are overlaid.