Description of reportEnzymeUsage

0001 function usageReport = reportEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)
0002 % reportEnzymeUsage
0003 %   Summarizes the results from enzymeUsage.
0004 %
0005 %  Input:
0006 %   ecModel         a GECKO3 ecModel
0007 %   usageData       output from enzymeUsage
0008 %   highCapUsage    minimum ratio of enzyme capacity usage to be considered
0009 %                   as high usage (Optional, default 0.9, refering to a
0010 %                   minimum of 90% capacity usage)
0011 %   topAbsUsage     number of top enzymes with highest absolute usage
0012 %                   (Optional, default 10, returning the top 10 enzymes
0013 %                   with highest absolute usage. With Inf or 0, all enzymes
0014 %                   are returned)
0015 %
0016 %  Output:
0017 %   usageReport     table with summary information
0018 %
0019 % Usage:
0020 %   usageReport = reportEnzymeUsage(ecModel, usageData, highCapUsage)
0021 
0022 if nargin < 3 || isempty(highCapUsage)
0023     highCapUsage = 0.9;
0024 end
0025 if nargin < 4 || isempty(topAbsUsage)
0026     topAbsUsage = 10;
0027 end
0028 
0029 usageReport = {};
0030 
0031 % Highest capacity usage
0032 highUsageProt = find(usageData.capUsage > highCapUsage);
0033 highEnzyme    = usageData.protID(highUsageProt);
0034 [~,enzIdx]    = ismember(highEnzyme,ecModel.ec.enzymes);
0035 geneIDs       = ecModel.ec.genes(enzIdx);
0036 
0037 highUsage.protID     = {};
0038 highUsage.geneID     = {};
0039 highUsage.absUsage   = [];
0040 highUsage.capUsage   = [];
0041 highUsage.kcat       = [];
0042 highUsage.source     = {};
0043 highUsage.rxnID      = {};
0044 highUsage.rxnNames   = {};
0045 highUsage.grRules    = {};
0046 
0047 for i=1:numel(enzIdx)
0048     [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,ecModel.ec.enzymes(enzIdx(i)));
0049     % See if all reactions carried flux
0050     [~,rIdx] = ismember(rxns,ecModel.rxns);
0051     carriedFlux = usageData.fluxes(rIdx) > 1e-7;
0052     if isscalar(find(carriedFlux))
0053         highUsage.protID(end+1,1)      = highEnzyme(i);
0054         highUsage.geneID(end+1,1)      = geneIDs(i);
0055         highUsage.absUsage(end+1,1)    = usageData.absUsage(enzIdx(i));
0056         highUsage.capUsage(end+1,1)    = usageData.capUsage(enzIdx(i));
0057         highUsage.kcat(end+1,1)        = kcat(carriedFlux);
0058         highUsage.source(end+1,1)      = ecModel.ec.source(idx(carriedFlux));
0059         highUsage.rxnID(end+1,1)       = rxns(carriedFlux);
0060         highUsage.rxnNames(end+1,1)    = rxnNames(carriedFlux);
0061         highUsage.grRules(end+1,1)     = grRules(carriedFlux);
0062     else
0063         % Add one entry for combined usage
0064         highUsage.protID(end+1,1)      = highEnzyme(i);
0065         highUsage.geneID(end+1,1)      = geneIDs(i);
0066         highUsage.absUsage(end+1,1)    = usageData.absUsage(enzIdx(i));
0067         highUsage.capUsage(end+1,1)    = usageData.capUsage(enzIdx(i));
0068         highUsage.kcat(end+1,1)        = nan;
0069         highUsage.source{end+1,1}      = '===';
0070         highUsage.rxnID{end+1,1}       = '===';
0071         highUsage.rxnNames{end+1,1}    = 'involved in multiple rxns, usage combined, individual rxns below';
0072         highUsage.grRules{end+1,1}     = '===';
0073         % Recalculate reaction-specific usage
0074 
0075         rIdx = rIdx(carriedFlux);
0076         enzFlux = usageData.fluxes(rIdx);
0077         enzMet = strcat('prot_',highEnzyme{i});
0078         [~, enzEcIdx] = ismember(enzMet,ecModel.mets);
0079         indAbsUse = full(transpose(-ecModel.S(enzEcIdx,rIdx)).*enzFlux);
0080         indCapUse = (indAbsUse /sum(indAbsUse)) * usageData.capUsage(enzIdx(i));
0081 
0082         rxnNumber = length(rIdx);
0083         highUsage.protID(end+1:end+rxnNumber,1)      = highEnzyme(i);
0084         highUsage.geneID(end+1:end+rxnNumber,1)      = geneIDs(i);
0085         highUsage.absUsage(end+1:end+rxnNumber,1)    = indAbsUse;
0086         highUsage.capUsage(end+1:end+rxnNumber,1)    = indCapUse;
0087         highUsage.kcat(end+1:end+rxnNumber,1)        = kcat(carriedFlux);
0088         highUsage.source(end+1:end+rxnNumber,1)      = ecModel.ec.source(idx(carriedFlux));
0089         highUsage.rxnID(end+1:end+rxnNumber,1)       = rxns(carriedFlux);
0090         highUsage.rxnNames(end+1:end+rxnNumber,1)    = rxnNames(carriedFlux);
0091         highUsage.grRules(end+1:end+rxnNumber,1)     = grRules(carriedFlux);
0092     end    
0093 end
0094 
0095 usageReport.highCapUsage = struct2table(highUsage);
0096 
0097 % Highest absolute usage
0098 [~,topUse]          = sort(usageData.absUsage,'descend');
0099 topEnzyme           = usageData.protID(topUse(1:topAbsUsage));
0100 [~,b]       = ismember(topEnzyme,ecModel.ec.enzymes);
0101 geneIDs     = ecModel.ec.genes(b);
0102 topUsage.protID     = {};
0103 topUsage.geneID     = {};
0104 topUsage.absUsage   = [];
0105 topUsage.percUsage  = [];
0106 topUsage.kcat       = [];
0107 topUsage.source     = {};
0108 topUsage.rxnID      = {};
0109 topUsage.rxnNames   = {};
0110 topUsage.grRules    = {};
0111 
0112 protPool = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'));
0113 
0114 for i=1:numel(topEnzyme)
0115     [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
0116     % See if all reactions carried flux
0117     [~,rIdx] = ismember(rxns,ecModel.rxns);
0118     carriedFlux = usageData.fluxes(rIdx) > 1e-7;
0119     if isscalar(find(carriedFlux))
0120         topUsage.protID(end+1,1)      = topEnzyme(i);
0121         topUsage.geneID(end+1,1)      = geneIDs(i);
0122         topUsage.absUsage(end+1,1)    = usageData.absUsage(topUse(i));
0123         topUsage.percUsage(end+1,1)   = topUsage.absUsage(end,1)/protPool*100;
0124         topUsage.kcat(end+1,1)        = kcat(carriedFlux);
0125         topUsage.source(end+1,1)      = ecModel.ec.source(idx(carriedFlux));
0126         topUsage.rxnID(end+1,1)       = rxns(carriedFlux);
0127         topUsage.rxnNames(end+1,1)    = rxnNames(carriedFlux);
0128         topUsage.grRules(end+1,1)     = grRules(carriedFlux);
0129     else
0130         % Add one entry for combined usage
0131         topUsage.protID(end+1,1)      = topEnzyme(i);
0132         topUsage.geneID(end+1,1)      = geneIDs(i);
0133         topUsage.absUsage(end+1,1)    = usageData.absUsage(topUse(i));
0134         topUsage.percUsage(end+1,1)   = topUsage.absUsage(end,1)/protPool*100;
0135         topUsage.kcat(end+1,1)        = nan;
0136         topUsage.source{end+1,1}      = '===';
0137         topUsage.rxnID{end+1,1}       = '===';
0138         topUsage.rxnNames{end+1,1}    = 'involved in multiple rxns, usage combined, individual rxns below';
0139         topUsage.grRules{end+1,1}     = '===';
0140         % Recalculate reaction-specific usage
0141         rIdx = rIdx(carriedFlux);
0142         enzFlux = usageData.fluxes(rIdx);
0143         enzMet = strcat('prot_',topEnzyme{i});
0144         [~, enzIdx] = ismember(enzMet,ecModel.mets);
0145         indUse = full(transpose(-ecModel.S(enzIdx,rIdx)).*enzFlux);
0146         rxnNumber = length(rIdx);
0147         topUsage.protID(end+1:end+rxnNumber,1)      = topEnzyme(i);
0148         topUsage.geneID(end+1:end+rxnNumber,1)      = geneIDs(i);
0149         topUsage.absUsage(end+1:end+rxnNumber,1)    = indUse;
0150         topUsage.percUsage(end+1:end+rxnNumber,1)   = topUsage.absUsage(end-(rxnNumber-1):end,1)/protPool*100;
0151         topUsage.kcat(end+1:end+rxnNumber,1)        = kcat(carriedFlux);
0152         topUsage.source(end+1:end+rxnNumber,1)      = ecModel.ec.source(idx(carriedFlux));
0153         topUsage.rxnID(end+1:end+rxnNumber,1)       = rxns(carriedFlux);
0154         topUsage.rxnNames(end+1:end+rxnNumber,1)    = rxnNames(carriedFlux);
0155         topUsage.grRules(end+1:end+rxnNumber,1)     = grRules(carriedFlux);
0156     end
0157 end
0158 usageReport.topAbsUsage     = struct2table(topUsage);
0159 usageReport.totalUsageFlux  = protPool;
0160 end
reportEnzymeUsage

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
