4. Compute chokepoints

Given a genome-scale model in SBML format, findCPcli computes chokepoints, dead-end metabolites, essential reactions, and essential genes, and saves the results in a spreadsheet. findCPcli can be run as follows, where model.xml is the file with the SBML model and results.xls is the file where the results will be saved.

$ findCPcli -i model.xml -o results.xls

The following figure shows the pipeline of the chokepoint computation process. For a given SBML file, computations are performed on 4 models: i) model in the SBML file; ii) model without DEM; iii) model refined with FVA, i.e. with flux bounds updated according to FVA; and iv) model refined with FVA and without DEM.

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4.1. Spreadsheet data

The previous command produces a spreadsheet file containing the following sheets:

  • model_info: General model information.

  • reactions: List of reactions of the model

  • metabolites: List of metabolites of the model

  • genes: List of genes of the model

  • reactions_FVA: Upper and lower flux bound of each reaction obtained with Flux Variability Analysis.

  • metabolites_FVA: Upper and lower flux bound of each reaction obtained with Flux Variability Analysis grouped by metabolite.

  • reversible_reactions: List of reversible reactions of the model before and after FVA refinement.

  • chokepoints: Chokepoint reactions and the metabolite/s they produce/consume. Chokepoints are computed in 4 different models:

    1. Input model in the SBML file.

    2. Model without DEM.

    3. Model refined with FVA.

    4. Model refined with FVA and without DEM.

  • dead-end: Dead-end metabolites before and after FVA refinement.

  • essential genes: List of essential genes of the model. Essential genes are computed in the 4 previously listed models.

  • essential reactions: List of essential reactions of the model. Essential reactions are computed in the 4 previously listed models.

  • comparison: Comparison of chokepoint, essential reactions and essential gene reactions in the 4 previously listed models.

  • summary: Comparison the size of the previous sets and their intersections.