Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. The evolution of generic human GEMs.
  • Fig. S2. Replication of infant growth simulation using Human1.
  • Fig. S3. Memote report screenshot for Human1.
  • Fig. S4. Human1 quality and performance over the curation process.
  • Fig. S5. Labeled 2D tSNE projection of tissue- and tumor-specific GEM reaction content comparison based on Hamming similarity.
  • Fig. S6. Visualization of altered proline metabolism in CHOL using Metabolic Atlas.
  • Fig. S7. Visualization of increased expression in fatty acid beta oxidation subsystems for LAML using Metabolic Atlas.
  • Fig. S8. Enrichment of true positives in model-predicted essential genes.
  • Fig. S9. Comparison of gene essentiality predictions among the three reference GEMs and their 621 derivative cell line models with CRISPR knockout screen results from the DepMap database.
  • Fig. S10. Impact of gene essentiality threshold on DepMap gene essentiality analysis results.
  • Fig. S11. Gene essentiality predictions when considering only biomass production compared to considering the activity of 57 different metabolic tasks.
  • Fig. S12. Effect of enzyme constraints on GEM flux variability.
  • Table S1. Comparison of generic human GEM statistics.
  • Table S2. Issue-guided model curation workflow implemented on the Human-GEM GitHub repository.
  • Table S3. Summary of model changes associated with each version of Human-GEM.
  • Legends for data files S1 to S5
  • References (5672)

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (Microsoft Excel format). Composition of the generic human cell biomass reaction.
  • Data file S2 (Microsoft Excel format). Average fatty acid composition for the curation of lipid metabolism.
  • Data file S3 (Microsoft Excel format). Metabolic tasks required for cellular viability.
  • Data file S4 (Microsoft Excel format). FVA of ecGEMs.
  • Data file S5 (Microsoft Excel format). NCI-60 cell line experimental exchange fluxes.