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Overview of the Pathway Tools FBA Module

Overview of the Pathway Tools FBA Module. The Pathway Tools Approach to FBA: FBA Model as a Database. Store and update metabolic model within Pathway Tools PGDB Export to constraint solver for model execution Fast generation of metabolic model from annotated genome

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Overview of the Pathway Tools FBA Module

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  1. Overview of the Pathway Tools FBA Module

  2. The Pathway Tools Approach to FBA: FBA Model as a Database • Store and update metabolic model within Pathway Tools PGDB • Export to constraint solver for model execution • Fast generation of metabolic model from annotated genome • PGDB associates a wealth of information with FBA model • Chemical structures • The genome • Regulatory information • Literature citations • Evidence codes • Pathway definitions • Unique identifiers for each component of the model are used consistently across multiple PGDBs/models

  3. The Pathway Tools Approach to FBA • Extensive query and visualization tools • Visualize individual metabolites, reactions, pathways • Metabolite page shows all reactions and transporters that act on that metabolite • Visualize reaction flux and omics data using Cellular Overview • Unique Cellular Overview generated for each PGDB • Debug/validate model using Pathway Tools • Dead-end metabolite analysis • Visual inspection on cellular overview • Reachability analysis • Store conditions of growth/non-growth in PGDB • Store knock-out phenotypes in PGDB

  4. The Pathway Tools Approach to FBA • Multiple gap filling approach • Gap-fill reactions, reaction directions, nutrients, secretions, biomass metabolites • Combine automated and manual analysis for maximum accuracy

  5. SRI FBA Results:E. coli Model • 1330 reactions in the EcoCyc PGDB • 370 reactions carry flux to produce 58 biomass metabolites • Model validated using the same knock-out data as used in Feist 2007 • Our model: 86.1% accuracy on 873 genes • Feist et al 2007: 90.6% accuracy on same 873 genes

  6. SRI FBA Results:Homo Sapiens Model • 1720 reactions in PGDB • 236 reactions carry flux to produce 51 biomass metabolites • ~6 reactions suggested by gap filler were supported by literature research • Several suggested changes in reaction direction also supported by literature research

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