Fig. 2

Identifying environment-reaction associations. A Residual reaction frequencies predicted from the collection of panEFMs that exist across the 208 environments that support the growth of the toy pan-reactome (Fig. 1C). The residuals are the difference between the average frequency over the collection of panEFMs defined within each environment and the average across all environments. Reactions along the x-axis are sorted by the environment-driven score (EDS), see text for details; B Metabolite-reaction association matrix defined by the pairwise correlation between the metabolites and reactions with non-zeros residuals; C Subnetworks generated from the rows of the metabolite-reaction association matrix (shown in B), showing the positive (+) and negative (−) associations between metabolite usage and reaction frequencies in panEFMs; D, E Elastic net prediction of the metabolite usage that evolved in a simulation of a Moran-like process. The evolved reaction frequencies were used to predict how the resulting strains use metabolites in their environments (y-axis) and compared to their usage in the simulated environment (x-axis)