Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases
Fig 3
Edge inference assessment on simulated networks (A) with complete knowledge of regulatory interactions, and on yeast (B and C) where very limited examples were known. ROC curves illustrate performance for inferred edges pooled from all 25 simulated networks, each containing 100 nodes. Different types of regulation were assessed independently as indicated in the legend. Gene set ‘V’ refers to any gene. Area proportional diagrams for yeast inference are shown in (B). Gray areas represent the proportion of predicted interactions relative to the total possible for each type. Performance on the validation set (Known) are shown as colored areas representing the proportion of the known interactions that were predicted (or not predicted) for the two types of secondary regulation, d(P, T) in red and d(P, P) in blue. The counts of each interaction type are also shown next to each of the four areas in the two proportional diagrams. Fisher’s exact test p-values represent the chance of observing the prediction performance by random chance. Odds ratio for the number of shared GO Biological Process (BP) terms between interacting genes (C) based on the number of shared GO terms for inferred compared to uninferred edges. Dashed lines show the 95% confidence intervals of the odds ratios.