Supplementary Figure 2 from Metabolic Associations of Reduced Proliferation and Oxidative Stress in Advanced Breast Cancer

PDF file, 427K, MPA example. An example of MPA computation based on a metabolic model and gene-expression or protein abundance measurements. Circular nodes represent metabolites, whereas diamond nodes represent enzymes. For enzymes, gray, red and green represent normal, significantly high and significantly low expression of the enzyme or enzyme-encoding genes, respectively. Similarly, for reactions, those that are predicted as active, inactive or undetermined are colored red, green, or gray, respectively. Solid edges represent metabolic reactions. Broken edges associate enzymes with the reactions they catalyze. The optimal solution obtained for a given sample with (B, D) or without (A, C) the additional constraint to activate the metabolic process of M9 production is shown. The score of the solution is the sum of reactions that are consistent with their expression state, which is what we aim to maximize. The MPA score of a given sample and a metabolic process is then the ratio between the optimal scores obtained with and without the process activity. As each sample has its unique expression profile, different MPA scores are obtained: The M9 production MPA score of sample 1 is smaller than that of sample 2, as its expression is less consistent with M9 production (i.e., enzymes E5 and E7 are lowly expressed).