Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks

doi:10.1371/journal.pcbi.1014066

Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks

Fig 3

Enrichment analysis for reactions with well-predicted fluxes.

A. Comparison of a predicted and estimated flux distribution for a representative knock-out strain, pgi6. The fluxes are logarithmically transformed, with a small constant () added to all values to avoid taking the logarithm of zero. The Pearson correlation between the predicted and estimated fluxes is 0.87 (p-value = 0.0). A prediction interval band, corresponding to a 90% confidence level, is depicted in light blue. The reactions inside this interval band are considered to have well-predicted fluxes. Highlighted reactions outside of the confidence region include: TPI_b (Triose-phosphate isomerase), ADK1 (Adenylate kinase), PPM_b (Phosphopentomutase), GSNK (Guanosine kinase), NTD9 (5’-nucleotidase (GMP)), ADK3 (Adentylate kinase (GTP)), NACODA (N-acetylornithine deacetylase), and EDA (2-dehydro-3-deoxy-phosphogluconate aldolase) B. The mean and standard deviation of the proportions of reactions with well-predicted fluxes across subsystems for all knock-out strains. The value above each bar indicates the number of knockout strains in which the corresponding metabolic subsystem is significantly enriched with reactions exhibiting well-predicted fluxes, determined using a hypergeometric test with Bonferroni-corrected p-values below the 0.02 significance threshold.

doi: https://doi.org/10.1371/journal.pcbi.1014066.g003