Perturbation effects on phenotype changes in E. coli . (A) A subset of the engineering metrics associated with E. coli phenotype clusters (meta-phenotypes) shown in Figure2. For values of engineering metrics (z-scores) and cluster sizes, refer to legend in Figure2. (B) Meta-phenotype transition network for E. coli. Nodes i and j represent two viable-growth engineering meta-phenotypes (the nonviable-growth meta-phenotype is not shown). Node labels correspond to Clusters shown in (A). Node sizes are proportional to cluster sizes shown in (A). Edge t
represents the cumulative phenotype-cluster transition frequency between Nodes i and j due to a specified perturbation type. Edges are bidirectional, so t
is equivalent to t
. Edge thickness is proportional to the cumulative transition frequency for environmental or genetic perturbations. Edges with relative frequency < 1% have been filtered out, primarily omitting low relative frequency single and double gene-deletion perturbations. (C) Legend for meta-phenotype transition network in (B). Node faces are divided into quadrants that correspond to the selected engineering metrics shown in (A). Quadrant colors indicate the associated metric z-scores for the corresponding Cluster. Perturbation type (edge attribute) abbreviations: C = carbon sources, EA = electron acceptor sources, N = nitrogen sources, P = phosphorous sources, S = sulfur sources, SGD = single gene deletions, and DGD = double gene deletions.