Efmviz

efmBackboneExtraction(EFMRxns, percentage)[source]

This function extracts all the reactions present in a certain percentage of EFMs

USAGE:

[selectedRxns, rxnDistribution] = efmBackboneExtraction (EFMRxns, percentage)

INPUTS:

  • EFMRxns – matlab array containing reactions in EFMs (each row is an EFM and every entry indicates the reaction IDs in the EFM)

  • percentage – a number indicating the cut off percentage. The reactions which are present in >= ‘percentage’ number of EFMs will be returned as output. ex. ‘80’

OUTPUTS:

  • selectedRxns – table of reactions which are present in >= ‘percentage’ number of EFMs. The columns in the table are:

    • rxnID - reaction ID

    • numEFMOccurrence - the number of EFMs the reaction occurs in

    • efmOccPercentage - percentage of EFMs the reaction occurs in. Calculated as: efmOccPercentage = numEFMOccurrence/<totalNumberOfEFMs> * 100

  • rxnDistribution – table of all reactions which are present in the input set of EFMs. The columns in the table are:

    • rxnID - reaction ID

    • numEFMOccurrence - the number of EFMs the reaction occurs in

    • efmOccPercentage - percentage of EFMs the reaction occurs in. Calculated as: efmOccPercentage = numEFMOccurrence/<totalNumberOfEFMs> * 100

efmEnrichmentAnalysis(EFMRxns, model, exprData, GSCFileName, GSSFileName, minSum)[source]

This function performs preprocessing for EFM enrichment. Two input files will be generated: Gene Set Collection (GSC) file: The gene set collection should describe the grouping of reactions into EFMs.

A two-column (space-separated) file: <EFM name or number> and <reaction ID> will be generated.

Gene Set Statistics (GSS) file: The gene set collection should contain a p-value and expression value for each reaction.

Gene level statistics will be mapped from genes onto the reactions using the GPR rules defined in the model. A three-column (space-separated) file: <reaction ID> <fold change> <p value> will be generated.

USAGE:

efmEnrichmentAnalysis (EFMRxns, model, exprData, GSCFileName, GSSFileName)

INPUTS:

  • EFMRxns – matlab array containing reactions in EFMs (each row is an EFM and every entry indicates the reaction IDs in the EFM)

  • model – COBRA model structure with fields:

    • .rxns - n x 1 cell array of reaction identifiers

  • exprData – mRNA expression data structure .gene cell array containing GeneIDs in the same

    format as model.genes

    .value Vector containing corresponding expression

    value (FPKM/RPKM)

  • exprSig Vector containing corresponding significance values

  • GSCFileName – file name of GSC file

  • GSSFileName – file name of GSS file

OPTIONAL INPUTS:

minSum – boolean flag for how GPR rule must be used. ‘false’ means use min for AND and max for OR (default), ‘true’ means use min for AND and Sum for OR

OUTPUTS:

Two files GSC File and GSS File are written in the working directory

efmFilter(EFMRxns, roi)[source]

This function returns a subset of EFMs that contain a desired reaction of interest

USAGE:

[filteredEFMs, row] = efmFilter (EFMRxns, roi)

INPUTS:

  • EFMRxns – matlab array containing reactions in EFMs (as returned by the function importEFMs)

  • roi – (numeric) index of the reaction of interest as in the input model

OUTPUTS:

filteredEFMs – matlab array containing subset of EFMs that contain ‘roi’

OPTIONAL OUTPUTS:

row: indices of EFMs that were filtered

Example

filteredEFMs = efmFilter(EFMRxns, 729); % 729 is the ID for acetate release reaction in the iAF1260 model

efmImport(EFMfileLocation, EFMFileName, EFMFluxfileLocation, EFMFluxFileName)[source]

This function reads the file containing all EFMs

USAGE:

[EFMRxns, EFMFluxes] = efmImport (EFMfileLocation, EFMFileName, EFMFluxfileLocation, EFMFluxFileName)

INPUTS:

  • EFMfileLocation – location of the file containing all EFMs

  • EFMFileName – name of the file containing all EFMs <name.txt>

OPTIONAL INPUTS:

  • EFMFluxfileLocation – location of the file containing relative fluxes of EFMs

  • EFMFluxFileName – name of the file containing relative fluxes of EFMs <name.txt>

OUTPUTS:

EFMRxns – matlab array containing reactions in EFMs. Each row corresponds to an EFM and contains indices of reactions active in the EFM

OPTIONAL OUTPUTS:
EFMFluxes: matlab array containing reaction fluxes in EFMs.

rows = EFMs and columns = reactions. Each entry contains (relative) fluxes of reactions active in that EFM, zeros otherwise

Example

EFMRxns = efmImport(‘C;/Analysis/’, ‘testEFMs.txt’); EFMRxns = efmImport(‘’, ‘test.txt’); % when the file is in the current directory [EFMRxns, EFMFluxes] = efmImport(‘C;/Analysis/’, ‘testEFMs.txt’, ‘C;/Analysis/’, ‘testFluxes.txt’); ; % with optional inputs

efmSubmodelExtractionAsSBML(model, rxnsForSubmodel, outputFileName, remFlag, ubiquitousMets)[source]

This function takes an input array containing reaction indices (in an EFM) and extracts as a sub-model (SBML file) which can be visualised in Cytoscape

USAGE:

  • modelEFM = efmSubmodelExtractionAsSBML (model, rxnsForSubmodel, outputFileName)

  • modelEFM = efmSubmodelExtractionAsSBML (model, rxnsForSubmodel, outputFileName, remFlag, ubiquitousMets)

INPUTS:

  • model – COBRA model that was used for EFM calculation, with fields:

    • .rxns - n x 1 cell array of reaction identifiers

    • .mets - m x 1 cell array of metabolite identifiers

  • rxnsForSubmodel – array of reaction indices (such as those in an EFM)

  • outputFileName – file name of the output sbml file e.g., <name>.xml

OPTIONAL INPUTS:

  • remFlag – boolean indicating whether ubiquitous metabolites should be removed

  • ubiquitousMets – list of metabolites to remove. An example list of ubiquitous metabolites: ubiquitousMets = {‘h’;’h2’;’fe3’;’fe2’;’h2o’;’na1’;’atp’;’datp’;’hco3’;’pi’;’adp’;’dadp’;’nadp’;’nadph’;’coa’;’o2’;’nad’;’nadh’;’ppi’;’pppi’;’amp’;’so4’;’fad’;’fadh2’;’udp’;’dudp’;’co2’;’h2o2’;’nh4’;’ctp’;’utp’;’gtp’;’cdp’;’gdp’;’dcdp’;’dgdp’;’dtdp’;’dctp’;’dttp’;’dutp’;’dgtp’;’cmp’;’gmp’;’ump’;’dcmp’;’dtmp’;’dgmp’;’dump’;’damp’;’cl’};

OUTPUTS:

modelEFM – submodel containing reactions, metabolites and genes in the EFM of interest

Example

rxnsForSubmodel = [1 2 3 4 5]; % select first 5 reactions modelEFM = efmSubmodelExtractionAsSBML(model, rxnsForSubmodel, outputFileName);

efmSubsystemsExtraction(model, EFMRxns)[source]

This function finds all unique subsystems in the input set of EFMs

USAGE:

[subsysSummary, uniqSubsys, countSubPerEFM] = efmSubsystemsExtraction (model, EFMRxns)

INPUTS:

  • model – COBRA model that was used for EFM calculation, with fields:

    • .subSystems - m x 1 cell array of subsystem name(s) per reaction

  • EFMRxns – matlab array containing reactions in EFMs (as returned by the function efmImport)

OUTPUTS:

  • subsysSummary – table (from tabulate) of the unique subsystems present in the input EFMs, sorted by descending occurrence count, with columns for subsystem name, count, and percentage

  • uniqSubsys – cell array of unique, non-empty subsystem names found among the reactions in the input EFMs

  • countSubPerEFM – numel(uniqSubsys) x size(EFMRxns, 1) matrix; each entry is the number of reactions belonging to that subsystem in the corresponding EFM

efmYieldAnalysis(EFMFluxes, uptkRxnID, relRxnID)[source]

This function performs yield analysis on the input set of EFMs

USAGE:

EFMyield = efmYieldAnalysis (EFMFluxes, uptkRxnID, relRxnID)

INPUTS:

  • EFMFluxes – matlab array containing relative fluxes of reactions in EFM

  • uptkRxnID – (numeric) index of the desired uptake reaction as in the input model

  • relRxnID – (numeric) index of the desired release reaction as in the input model

OUTPUTS:

EFMyield – matlab array with yields for all input set of EFMs

Example

EFMyield = efmYieldAnalysis(EFMFluxes, 729, 889); % 729 is the ID for acetate release reaction in the iAF1260 model