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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Multiplex methods provide effective integration of multi-omic data in genome-scale models

Fig. 3

The 2369 Colombos gene expression microarray profiles mapped to the tridimensional space of objective functions biomass-acetate-formate (top four panels) and biomass-succinate-ethanol (bottom four panels) using trilevel linear programming (Eqs. (2-3)). Each gene expression profile is translated into flux bounds using (3); then, the trilevel problem (2) is solved with biomass-acetate-formate and biomass-succinate-ethanol as objectives, thus obtaining a point in each of the two objective spaces. In both objective spaces, we show the conditions mapped to the full space (top left), and the projections to the three two-dimensional subspaces: first-second objectives (top right), second-third objectives (bottom left), first-third objectives (bottom right). We also find the trade-off between the two objectives shown in each subspace, across the sets of aerobic and anaerobic conditions. The color scale shows the value of the third objective in each point. Among the 2369 conditions (obtained with different pH, antibiotics, heat shock, glucose concentrations), 128 conditions are anaerobic. The plot also shows the subspace where E. coli operates in both the objective spaces selected and allows cross comparing the metabolic flexibility when production of different metabolites is required simultaneously

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