Fig. 5: Integrating experimental kinetic information improves other parameter estimates.

a, The OS (defined in d) of RENAISSANCE estimates for 17 experimentally available Michaelis constants, K_Ms, from TCA (red). The estimation process involved integrating experimental values for 9 out of the 17 parameters and estimating other model parameters including the remaining 8 parameters from TCA. The procedure was repeated ten times with a different random combination of nine parameters. The black diamonds represent the OS of the estimates without integrating experimental data. The error bars indicate the standard error in the OS over ten combinations of integrated parameters. b, The mean OS for the estimated K_Ms within metabolic subsystems before (blue) and after (red) integrating experimentally measured K_Ms. The estimation process for each subsystem was conducted in a similar manner as in a. c, The OS of RENAISSANCE estimates for 91 experimentally available K_Ms not belonging to TCA when 10 different combinations of 9 (out of 17) K_Ms from TCA were integrated. The black diamonds represent the OS without integration. The error bars represent the standard error in OS. d, The mean OS of the estimated K_Ms from all metabolic subsystems except for the subsystem labelled on the x axis before (blue) and after (red) integrating K_Ms from the labelled subsystem. e, The metabolic subsystems of the top 15 K_Ms with the highest increase in OS when Michaelis constants from the labelled subsystem were integrated. The donut plots indicate the count of integrated experimental K_M values from each labelled subsystem. f, The two-component PCA⁴⁸ representation of the 276 (out of 384) experimentally unverified kinetic parameters with and without integrating experimentally measured Michaelis constants. g, The OS of an estimated K_M is calculated as the ratio between (x) the overlap of the RENAISSANCE predicted (teal) and the experimentally observed range (violet), and (y) the RENAISSANCE predicted range. anpl, anaplerotic reactions; glu, glutamate metabolism; gly, glycolysis/gluconeogenesis; glse, glycine/serine metabolism; hist, histidine metabolism; nsp, nucleotide salvage pathway; oxp, oxidative phosphorylation; pyr, pyruvate metabolism; shkk, shikimate pathway; oth, other reactions.