Fig. 4

Various results of expression data interpretation through context-specific PC-model. a Is a selected collection of PC-FVA results across 16 samples regarding acetyl-CoA synthesis, ATP synthesis, De novo fatty acid synthesis (FAS), and TAG synthesis pathway reactions. The bar plot shows the variability of each metabolic reaction and is coupled to the left y-axis in mmol/gDW/h. Green, yellow, orange, and red bars reflect the flux variability at \(0\%\), \(50\%\), \(90\%\), and \(99\%\) of maximum TAG synthesis rate (i.e., EX_TAG flux), respectively. The black line plot shows the expression level of the reaction and is coupled to the right y-axis. In the case of isozymes presence, the black line plots the numerical sum of all isozyme levels. The calculated Spearman’s rank correlation (\(\rho\)) between the FVA result and expression is listed in the bracket. Vertical dashed lines divide time-series samples into pre-wash, N-free, and post-boost phases. b Demonstrates a simplified reaction network around FAS and the TAG synthesis pathway. Different fatty acid, their derivatives, and different TAG are not differentiated. c Shows the suggested overexpression level (folds) of the top 15 bottleneck proteins to maximize TAG production while minimizing deviation from the measured RNA-Seq (through the protein abundance constraints). Gene symbols and functional categories of each protein are shown to the left of each gene ID (row labels)