Intuitive Visualization and Analysis of Multi-Omics Data and Application to Escherichia coli Carbon Metabolism
Figure 1
All molecular or functional components of the metabolic and regulatory networks are explicitly represented using specific symbols. Each RNA (square) encodes a polypeptide (rounded square). Polypeptides or polypeptide complexes generate functional entities – i.e., enzymes or regulators – (hexagons). Enzymes catalyze reactions (circles), which allow the inter-conversion of metabolites (diamonds). A color code can be applied to each node (symbol) in the network to visualize experimental data (gene expression for the squares, protein abundance for the rounded squares, specific activity for the hexagons, metabolite concentrations for the diamonds and flux values for the circle). Interactions between the components are indicated with lines (edges). Four main kinds of interactions were considered and were represented using lines with specific colors: biochemical conversions (grey lines), transcriptional and translational regulations (blue lines), control of enzymatic activities by metabolic effectors or by phosphorylation (green lines), hierarchical relationships – i.e. RNAs to proteins, proteins to activities, activities to reactions - (pink lines). In the given example, a metabolite X is converted in Y through the reaction ECx.x.x.x. The reaction requires a molecule of H2O and produces a molecule of CO2. The metabolite W is a negative effector of this reaction. The reaction depends on the enzymatic activity “Actv” which is a property of the protein “Actv Prot”. This protein is encoded by the gene “Actv gene” whose transcription is induced by the activity “Trx° Factor”, itself resulting from the protein and gene “Trx°”. Translation of “Actv Prot” is controlled by the translation factor “Trl° Fact”.