FIGURE 1.

A schematic representation of systems approaches using functional genomics. (A) A protein–protein interaction network represents a global picture of a system at the protein level. In this example, several plant hub proteins (large blue circles) that interact with many plant proteins (small blue circles) are targeted by microbial effectors (large red circles). This approach was used in Mukhtar et al. (2011). (B) Gene regulatory network modeling infers regulatory relationships among components of a system. As an example, a network consisting of seven components (circles with different colors) with positive and negative regulatory relationships (red and blue lines, respectively) is depicted. This approach was used in Sato et al. (2010). (C) Co-expression module analysis is useful to visualize behavior of a system under certain conditions. As an example, co-regulated genes under different conditions are visualized in the heatmap. Red and green boxes indicate up-regulated and down-regulated genes in a certain condition, respectively. This approach was used in Zou et al. (2011), Atkinson et al. (2013), Prasch and Sonnewald (2013), and Rasmussen et al. (2013). (D) A ternary plot is used to show influence by three variables on composition. This example depicts bacterial OTUs whose relative abundance changes according to the three compartments, soil, rhizosphere, and root. Blue circles mark OTUs enriched in the root compartment. This approach was used in Bulgarelli et al. (2012) and Lundberg et al. (2012).