Fig. 1.

The transcriptomic and fluxomic layers of environmental conditions constitute our multiplex (duplex) network, where nodes are environmental conditions. The real-valued gene-reaction map φ converts gene set expression values into flux bounds for the trilevel FBA model of E. coli (see Methods). For each condition, the gene expression profile is mapped to the metabolic model, and a trilevel linear program is solved to calculate the condition-specific distribution of flux rates, therefore linking gene expression to phenotype. A network of conditions is then built independently in both layers. The multiplex network is then fused into a single network through our weighted network fusion approach. Finally, further learning is performed on the combined network to elucidate relations between conditions