Skip to main content
Figure 3 | Genome Biology

Figure 3

From: MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

Figure 3

MetaReg model canvas view of leucine biosynthesis in yeast during simulation of leucine starvation. The model includes the extracellular stimuli, leucine uptake into the cell by various permeases, the leucine biosynthetic pathway, and its transcriptional regulation by Leu3 and Gcn4. Variable name suffixes indicate variable types: 'm' represents mRNA and 'ap' represents active protein. Arrows indicate the direction of regulation. Arrow types represent either activation (→), repression () or other (-) of a variable; for complex logics, the arrow types are an approximation only. The logics of the regulation are not displayed in this view, but are accessible via other windows (Figure 2c). The model canvas enables highlighting of different sets of variables. In this snapshot, all the cycles in the model are highlighted in orange. The model is presented here during a simulation of leucine starvation: the values of the extracellular stimuli on variables NH3, amino acids, rapamycin and leucine were fixed to states 2, 2, 0, and 0, respectively. The resulting predicted (simulated) states of all other variables are presented to the left of their nodes.

Back to article page