Fig. 3
Monocyte-to-macrophage differentiation is accompanied by activation of alternative metabolic branches and increased activity of already active pathways. For each pathway, the level of activity (percentage of reactions in the input model that are present in the context-specific model) was computed for each time point (left panel). Each column represents the model built by the FASTCORMICS workflow for the given time point whereas each line stands for a different pathway. The fraction of active reactions ranges from 0 to 1 and is represented in shades of gray for low, yellow for intermediate and red for high number of active reactions per pathway. Additionally, (right panel) the significantly differentially expressed genes (FDR <0.05 and absolute log2 fold change > 1) were mapped to the models via the GPR rules. The percentage of up-regulated reactions in a pathway was computed after summing up the significantly up-regulated reactions. The number of significantly down-regulated reactions was then removed from this sum and the total was then normalized by the number of reactions in the pathway. The fraction of reactions associated with differentially expressed genes ranges between −0.7 for down-regulated pathways in blue and 0.9 for unregulated pathways in red. Only pathways that show a differential expression over time are represented