Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes #372
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* fix: loadDatabases check for duplicate protIDs (SysBioChalmers#349) * fix: prevent NaN in light ecModels (SysBioChalmers#346) * fix: calculateFfactor if paxDB has taxID !4 chars (SysBioChalmers#347) * fix: runDLKcat if path has spaces (SysBioChalmers#352) * refactor: FSEOF (SysBioChalmers#356) * fix: FSEOF to 0.9 of teorethical max prod * refactor: switch force objetive to target * fix: remove unnecesary function * fix: update input arguments * fix: temporal solution k-score * refactor: FSEOF * feat: add gene essentiality to FSEOF * fix: file writing * feat: add cutoff based on quantile * feat: report target transport reactions * refactor: add cutoff for essentiality * fix: bug identifying gene essentiality * doc: move installations instructions to wiki (SysBioChalmers#357) * move installation instructions to wiki * GECKOInstaller checks for latest GECKO version * fix: prevent duplications in protein pseudometabolites * minor fixes * doc: update documentation * doc: swap gitter for GitHub Discussions * fix: correct link to upgrade instructions * fix: synchronize STEP numbers protocol and paper --------- Co-authored-by: Albert Tafur Rangel <[email protected]>
…g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.
…g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.
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- use fluxes from usageData - give protein pool in usageReport instead of printing to command window
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Suggested changes applied:
@HossFir, can you check if this works for you? Should give the same results as your earlier code. |
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@edkerk Thanks for your suggestions! The results were somehow identical! I've attached two TopUsed Enzymes for you to review. |
edkerk
approved these changes
Apr 28, 2024
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This PR will be reverted, as the changes by #379 avoid this problem to occur. If kept, the new protein usage numbers would be too high, due to double counting vai the total protein usage and the protein specific usage reactions. |
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Description:
Issue:
The original implementation of
topEnzymeUsagefunction calculatesprotPoolby only considering theprot_pool_exchangeflux. However, this does not reflect the total enzymatic capacity used by the metabolic reactions, especially when proteomics data is integrated into the model.Enhancement:
The function has been enhanced to account for the fluxes of all
usage_prot_reactions, excluding the ones related tousage_prot_standard.Changes:
Flux Calculation Integration: The function now includes a call to
solveLP(ecModel)to calculate the flux distribution within the model.Targeted Flux Summation: After obtaining the flux distribution, the function identifies all
usage_prot_reactions while filtering out any that includestandardin their reaction IDs. Since this reaction was embedded intoProtein_pool_exchange.Adjusted
protPoolDefinition: The protein pool (protPool) is redefined to be the sum of theprot_pool_exchangeflux and the total usage fluxes.