Figure 1

An example to show how the HLMN is reformatted from the liver model. A) Three metabolic reactions in the liver model are shown on the left, where hgentis, o2, 4mlacac, h, hco3 and h2co3 are metabolites, [c] and [m] are the abbreviations of cell compartments "cytoplasm" and "mitochondrion" denoting where the corresponding metabolites appear. The first metabolic reaction represents that homogentisate in cytoplasm (hgentis[c]) is oxidated into 4-Maleylacetoacetate (4mlacac[c]) and hydrogen ion (h[c]); the second means that the hydrogen ion in cytoplasm (h[c]) is transported into mitochondrion (h[m]); the third represents that the hydrogen ion in mitochondrion (h[m]) reacts with bicarbonate (hco3[m]) to form carbonic acid (h2co3[m]). The network reformatted from these three metabolic reactions is shown on the right, where each node denotes a metabolite with the information of cell compartment where it appears, two nodes have a link if there is a chemical reaction such that one metabolite is substrate and another one is a product. B) The abbreviations of cell compartment and their corresponding full names.