Figure 2

Illustration of the gene coordination principal, using the LKR/SDH gene as an example. (A) Relationship between Pearson correlation and gene coordination values, exemplified for the LKR/SDH gene probed against the entire genome-wide set of Arabidopsis genes. Each blue dot represents the relationship between Pearson correlation (Y axis) and positive coordination (X axis), while each red dot represents the relationship between Pearson correlation (Y axis) and negative coordination (X axis), calculated across the entire set of 211 biological perturbations. The two green rectangles indicate areas containing genes pairs having high positive correlation and a significant negative coordination across the entire of biological perturbations (upper left rectangle) and vice versa (lower right rectangle). (B, C, D) Relationships between the expression differences of the LKR/SDH gene and three other representative genes across the entire set of 211 biological perturbations. Each black dot indicates the expression difference (treatment versus control) in response to a single specific biological perturbation. Black dots inside red circles indicate perturbations that contribute to a negative coordination, while black dots inside blue circles indicate perturbations that contribute to a positive coordination between each of the two compared genes. The Pearson correlation value is indicated on the top of each panel.