Create a generic subnetwork from Recon 3D

Author(s): Ines Thiele, Ronan M. T. Fleming, Systems Biochemistry Group, LCSB, University of Luxembourg.
Reviewer(s): Almut Heinken, Catherine M. Clancy, Laurent Heirendt, LCSB, University of Luxembourg.
In this tutorial, we show how to create a generic subnetwork from Recon 3D that can still perform all metabolic test functions as well as has physiologically defined ATP yield from defined carbon sources. The resulting model does not contain a specified list of reactions, except if they are still needed for the aforementioned tasks, and that is flux consistent.

EQUIPMENT SETUP

Initialize the COBRA Toolbox

Initialize the Cobra Toolbox using the initCobraToolbox function.
initCobraToolbox(false) % false, as we don't want to update

Setting the optimization solver

This tutorial will be run with a 'glpk' package, which is a linear programming ('LP') solver. The 'glpk' solver does not require additional installation or configuration.
% solverName='glpk';
However, for the analysis of large models such as Recon 3D, it is not recommended to use the 'glpk' package, but rather a commercial-grade solver, such as 'gurobi'.
For the analysis of a Recon model, change the solver to 'gurobi':
solverName = 'gurobi';
changeCobraSolver(solverName, 'LP');
> Gurobi interface added to MATLAB path.

PROCEDURE

Load the model
In this tutorial, the used model is the generic model of human metabolism, Recon 3D [1]. If Recon 3D is not available, use Recon 2 [2] provided in The COBRA Toolbox. Other COBRA models may be downloaded from the Virtual Metabolic Human website and saved to your preferred directory.
Before proceeding with the simulations, the path for the model needs to be defined.
global CBTDIR
 
fileName= 'Recon2.0model.mat'; % if using Recon 3 model, amend filename.
model = readCbModel([CBTDIR filesep 'test' filesep 'models' filesep fileName]);
model.csense(1:size(model.S,1),1) = 'E';
Set the lower bounds on all biomass reactions and sink/demand reactions to zero.
model.lb(find(ismember(model.rxns, 'biomass_reaction'))) = 0;
model.lb(find(ismember(model.rxns, 'biomass_maintenance_noTrTr'))) = 0;
model.lb(find(ismember(model.rxns, 'biomass_maintenance'))) = 0;
DMs = (strmatch('DM_', model.rxns));
model.lb(DMs) = 0;
Sinks = (strmatch('sink_', model.rxns));
model.lb(Sinks) = 0;
model.ub(Sinks) = 1000;
Identify the model reactions that are needed to ensure that all carbon sources result in a physiologically relevant ATP yield. (Note that this function uses sparseFBA, i.e., alternative solutions may exist but are not considered here.)
[Table_csourcesOri, TestedRxnsC, Perc] = testATPYieldFromCsources(model);
Warning: Reaction with the same name already exists in the model, updating the reaction
DM_atp_c_ h2o[c] + atp[c] -> adp[c] + h[c] + pi[c]
Identify the model reactions that are needed to ensure that all metabolic functions can have a non-zero flux. (Note that this function uses sparseFBA, i.e., alternative solutions may exist but are not considered here.) Applicable to Recon3 only.
if ~isempty(strfind(fileName, 'Recon3'))
[TestSolutionOri,TestSolutionNameClosedSinks, TestedRxnsClosedSinks, PercClosedSinks] = test4HumanFctExt(model, 'all', 0);
TestedRxns = unique([TestedRxnsC; TestedRxnsClosedSinks]);
TestedRxnsX = intersect(model.rxns,TestedRxns);
end
Next we remove all human metabolic reactions (HMRs) (i.e., those reactions originating from HMR 2.0 [3] and that start with 'HMR_') that are not needed for the aforementioned tasks. Applicable to Recon 3 only.
if ~isempty(strfind(fileName, 'Recon3'))
HMR = model.rxns(strmatch('HMR_',model.rxns));
HMR_NE = setdiff(HMR,TestedRxnsX);
model.lb(find(ismember(model.rxns,HMR_NE))) = 0;
model.ub(find(ismember(model.rxns,HMR_NE))) = 0;
end
We will also remove all drug module reactions, i.e., those ones with the term 'Xeno' in the subsystem, mostly originating from [4]. Applicable to Recon 3 only.
if ~isempty(strfind(fileName, 'Recon3'))
DM = model.rxns(strmatch('Xeno', model.subSystems));
model.lb(find(ismember(model.rxns, DM))) = 0;
model.ub(find(ismember(model.rxns, DM))) = 0;
DMt = (strmatch('Transport of Xenobiotic', model.rxnNames));
model.lb(DMt) = 0;
model.ub(DMt) = 0;
end
We will also remove all reactions from the 'Peptide metabolism' subsystem. Applicable to Recon 3 only.
if ~isempty(strfind(fileName, 'Recon3'))
DM = model.rxns(strmatch('Peptide metabolism',model.subSystems));
model.lb(find(ismember(model.rxns, DM))) = 0;
model.ub(find(ismember(model.rxns, DM))) = 0;
end
We will use the method FASTCORE, 'fastcc', to ensure a flux-consistent subnetwork [5].
param.epsilon = 1e-4;
param.modeFlag = 0;
param.method = 'fastcc'; %'null_fastcc'
printLevel = 2;
[fluxConsistentMetBool, fluxConsistentRxnBool, fluxInConsistentMetBool, fluxInConsistentRxnBool, modelOut] = findFluxConsistentSubset(model, param, printLevel);
7440 Total reactions 3260 Reversible reactions. 4180 Irreversible reactions. 5096 Flux consistent reactions, without flipping. 1266 Flux inconsistent irreversible reactions, without flipping. 1078 Flux inconsistent reactions, without flipping. 5237 Flux consistent reactions. 937 Flux inconsistent reversible reactions left to flip. 5239 Flux consistent reactions. 935 Flux inconsistent reversible reactions left to flip. 5241 Flux consistent reactions. 933 Flux inconsistent reversible reactions left to flip. 5245 Flux consistent reactions. 880 Flux inconsistent reversible reactions left to flip.
And remove the flux inconsistent reactions from the model.
modelConsistent = removeRxns(model,model.rxns(find(fluxInConsistentRxnBool)));
We will now update the GPR associations.
modelConsistent.genes = [];
modelConsistent.rxnGeneMat = [];
modelgrRule = modelConsistent.grRules;
for i = 1 : length(modelgrRule)
if ~isempty(modelgrRule{i})
modelConsistent = changeGeneAssociation(modelConsistent, modelConsistent.rxns{i}, modelgrRule{i});
end
end
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New gene 22305.2 added to model New gene 2182.1 added to model New gene 2180.1 added to model New gene 2181.2 added to model New gene 22305.1 added to model
New gene 51703.1 added to model
New gene 11001.1 added to model
New gene 2182.2 added to model
New gene 116285.1 added to model
New gene 5167.1 added to model
New gene 6785.1 added to model
New gene 1579.1 added to model
New gene 1962.1 added to model
New gene 2194.1 added to model
New gene 376497.2 added to model New gene 10999.1 added to model New gene 376497.1 added to model New gene 11000.1 added to model
New gene 10998.1 added to model
New gene 226.2 added to model New gene 226.1 added to model New gene 226.3 added to model New gene 230.1 added to model New gene 229.1 added to model
New gene 2203.1 added to model New gene 8789.1 added to model
New gene 5210.1 added to model New gene 5207.1 added to model New gene 5209.1 added to model New gene 5208.1 added to model
New gene 2235.1 added to model New gene 2235.2 added to model
New gene 10840.1 added to model
New gene 79901.1 added to model
New gene 197258.1 added to model
New gene 80308.1 added to model New gene 80308.2 added to model
New gene 2356.1 added to model
New gene 29988.1 added to model New gene 6514.1 added to model New gene 155184.1 added to model New gene 6518.1 added to model New gene 66035.1 added to model
New gene 200010.1 added to model
New gene 10841.1 added to model New gene 10841.2 added to model
New gene 10588.1 added to model
New gene 4522.1 added to model New gene 286297.1 added to model
New gene 25902.1 added to model
New gene 2519.1 added to model
New gene 2517.1 added to model
New gene 2271.1 added to model
New gene 2184.1 added to model
New gene 1468.1 added to model
New gene 2523.1 added to model
New gene 2525.1 added to model
New gene 10690.1 added to model
New gene 85365.1 added to model New gene 85365.2 added to model
New gene 9334.1 added to model New gene 2683.1 added to model New gene 8703.1 added to model New gene 8704.2 added to model New gene 8704.1 added to model
New gene 2819.1 added to model
New gene 2820.1 added to model
New gene 5832.1 added to model
New gene 132789.1 added to model New gene 10007.1 added to model
New gene 9563.1 added to model
New gene 2539.1 added to model
New gene 57818.1 added to model New gene 2538.1 added to model New gene 92579.1 added to model
New gene 2542.1 added to model
New gene 2593.1 added to model New gene 2593.2 added to model
New gene 9514.1 added to model
New gene 5476.1 added to model New gene 2720.1 added to model New gene 2588.1 added to model New gene 4758.1 added to model
New gene 2581.1 added to model
New gene 2583.1 added to model
New gene 2584.1 added to model New gene 2585.2 added to model New gene 2585.1 added to model
New gene 26290.1 added to model New gene 79695.1 added to model New gene 2589.1 added to model New gene 50614.1 added to model New gene 8693.1 added to model New gene 55568.2 added to model New gene 114805.1 added to model New gene 11226.1 added to model New gene 117248.1 added to model New gene 11227.1 added to model New gene 55568.1 added to model New gene 2590.1 added to model New gene 51809.1 added to model New gene 79623.1 added to model New gene 63917.1 added to model New gene 2591.1 added to model
New gene 2592.1 added to model New gene 2592.3 added to model New gene 2592.2 added to model
New gene 81031.1 added to model
New gene 6523.1 added to model
New gene 7360.1 added to model New gene 7359.1 added to model New gene 7360.2 added to model
New gene 8972.1 added to model
New gene 2597.1 added to model New gene 26330.1 added to model
New gene 2618.1 added to model New gene 2618.2 added to model
New gene 175.1 added to model
New gene 2629.2 added to model New gene 2629.3 added to model New gene 2629.4 added to model New gene 2629.5 added to model New gene 2629.1 added to model
New gene 26301.1 added to model
New gene 275.1 added to model New gene 2731.1 added to model New gene 2653.1 added to model
New gene 2651.1 added to model
New gene 55343.1 added to model
New gene 2673.1 added to model New gene 9945.1 added to model
New gene 7264.1 added to model
New gene 8836.1 added to model
New gene 79017.1 added to model
New gene 8908.1 added to model New gene 2998.1 added to model New gene 2992.1 added to model New gene 2997.1 added to model
New gene 2687.1 added to model
New gene 6470.1 added to model New gene 6470.2 added to model
New gene 6472.1 added to model
New gene 2717.1 added to model
New gene 2632.1 added to model
New gene 2990.1 added to model
New gene 4669.1 added to model
New gene 1798.1 added to model New gene 1798.2 added to model
New gene 56606.1 added to model New gene 154091.1 added to model New gene 11182.1 added to model New gene 56606.2 added to model New gene 144195.1 added to model
New gene 159963.1 added to model New gene 6526.1 added to model New gene 125206.1 added to model New gene 6524.1 added to model
New gene 178.4 added to model New gene 178.5 added to model New gene 178.1 added to model New gene 178.3 added to model New gene 178.2 added to model New gene 178.6 added to model
New gene 2752.1 added to model New gene 51557.1 added to model
New gene 5834.1 added to model New gene 5837.1 added to model New gene 5836.1 added to model
New gene 2729.1 added to model New gene 2730.1 added to model
New gene 2747.1 added to model New gene 2746.1 added to model
New gene 2744.1 added to model New gene 27165.2 added to model New gene 27165.1 added to model
New gene 5471.1 added to model
New gene 83733.1 added to model New gene 79751.1 added to model
New gene 2639.1 added to model New gene 2639.2 added to model
New gene 57084.1 added to model New gene 246213.1 added to model New gene 57030.1 added to model
New gene 197257.1 added to model New gene 197257.2 added to model
New gene 54363.1 added to model New gene 51179.2 added to model New gene 51179.1 added to model
New gene 2628.1 added to model
New gene 9380.1 added to model
New gene 2710.2 added to model New gene 2712.1 added to model New gene 2710.1 added to model New gene 2713.1 added to model
New gene 3029.1 added to model New gene 84264.2 added to model New gene 84264.1 added to model
New gene 6536.1 added to model New gene 6536.2 added to model
New gene 2762.1 added to model
New gene 2766.1 added to model New gene 51292.1 added to model New gene 51292.3 added to model New gene 51292.2 added to model
New gene 8833.1 added to model
New gene 5226.1 added to model
New gene 27232.1 added to model
New gene 57678.1 added to model
New gene 2936.1 added to model
New gene 7001.3 added to model New gene 5052.3 added to model New gene 2877.1 added to model New gene 2876.2 added to model New gene 5052.2 added to model New gene 2876.1 added to model New gene 5052.1 added to model New gene 7001.1 added to model New gene 2879.1 added to model New gene 7001.2 added to model
New gene 2878.1 added to model New gene 257202.1 added to model
New gene 10935.1 added to model New gene 10935.2 added to model
New gene 2937.1 added to model
New gene 2679.1 added to model New gene 2678.1 added to model New gene 2678.3 added to model New gene 2678.2 added to model
New gene 2977.1 added to model New gene 2983.1 added to model New gene 4882.2 added to model New gene 2982.1 added to model New gene 2974.1 added to model New gene 2986.1 added to model New gene 4882.1 added to model New gene 2984.1 added to model New gene 4881.1 added to model New gene 3000.1 added to model
New gene 9615.1 added to model
New gene 3251.1 added to model
New gene 761.1 added to model New gene 771.1 added to model New gene 377677.1 added to model New gene 762.1 added to model New gene 766.2 added to model New gene 23632.1 added to model New gene 766.1 added to model New gene 771.2 added to model New gene 759.1 added to model New gene 768.1 added to model New gene 760.1 added to model
New gene 53905.1 added to model New gene 50506.1 added to model New gene 53905.2 added to model
New gene 343.1 added to model
New gene 3028.1 added to model New gene 3033.1 added to model
New gene 3038.2 added to model New gene 3036.1 added to model New gene 3038.1 added to model New gene 3037.1 added to model
New gene 27235.1 added to model
New gene 6522.1 added to model New gene 83697.1 added to model New gene 6521.1 added to model New gene 6508.2 added to model New gene 6508.1 added to model
New gene 3098.3 added to model New gene 80201.1 added to model New gene 2645.3 added to model New gene 3098.4 added to model New gene 3099.1 added to model New gene 2645.2 added to model New gene 3098.5 added to model New gene 2645.1 added to model New gene 3098.1 added to model New gene 3101.1 added to model New gene 3098.2 added to model
New gene 3081.1 added to model
New gene 11112.1 added to model
New gene 3034.1 added to model
New gene 3067.1 added to model
New gene 495.1 added to model New gene 496.1 added to model
New gene 8942.1 added to model
New gene 3145.1 added to model
New gene 3157.1 added to model New gene 3157.2 added to model
New gene 3158.1 added to model
New gene 3155.1 added to model New gene 54511.1 added to model
New gene 3162.1 added to model New gene 3163.1 added to model
New gene 26062.1 added to model
New gene 6448.1 added to model
New gene 3290.2 added to model New gene 3290.1 added to model
New gene 3291.1 added to model
New gene 3292.1 added to model New gene 7923.1 added to model
New gene 3294.1 added to model
New gene 51478.1 added to model
New gene 3283.1 added to model
New gene 3284.1 added to model
New gene 80270.1 added to model
New gene 9016.1 added to model New gene 7352.2 added to model New gene 7352.1 added to model New gene 7351.1 added to model New gene 9016.2 added to model New gene 7350.1 added to model New gene 9481.1 added to model
New gene 57026.1 added to model
New gene 3421.2 added to model New gene 3420.3 added to model New gene 3419.1 added to model New gene 3420.1 added to model New gene 3421.1 added to model New gene 3420.2 added to model
New gene 3417.1 added to model
New gene 3418.1 added to model
New gene 7173.4 added to model New gene 7173.1 added to model New gene 7173.3 added to model New gene 7173.2 added to model New gene 7173.5 added to model
New gene 3425.1 added to model
New gene 586.1 added to model
New gene 587.1 added to model
New gene 8501.1 added to model
New gene 3614.1 added to model New gene 3615.1 added to model New gene 3614.2 added to model
New gene 55586.1 added to model
New gene 114134.1 added to model
New gene 3422.1 added to model New gene 91734.1 added to model
New gene 160728.1 added to model
New gene 8802.1 added to model New gene 8801.1 added to model
New gene 8803.1 added to model
New gene 6560.1 added to model New gene 10723.1 added to model New gene 9990.1 added to model
New gene 57468.1 added to model
New gene 3795.1 added to model New gene 3795.2 added to model
New gene 8564.1 added to model
New gene 3938.1 added to model
New gene 53.1 added to model
New gene 3931.1 added to model
New gene 2739.1 added to model
New gene 124637.1 added to model
New gene 4047.1 added to model
New gene 5321.1 added to model New gene 1178.1 added to model New gene 29124.1 added to model
New gene 51268.1 added to model
New gene 4023.1 added to model
New gene 3990.1 added to model
New gene 11343.1 added to model New gene 11343.2 added to model
New gene 50487.1 added to model
New gene 9388.1 added to model New gene 5407.1 added to model New gene 8513.1 added to model New gene 5408.1 added to model New gene 5406.1 added to model
New gene 9227.1 added to model
New gene 6309.1 added to model
New gene 4048.1 added to model
New gene 4056.1 added to model New gene 4259.1 added to model New gene 4056.2 added to model New gene 4258.1 added to model
New gene 4124.1 added to model New gene 4122.1 added to model
New gene 4245.1 added to model
New gene 11320.1 added to model New gene 11282.2 added to model New gene 11282.1 added to model
New gene 4248.1 added to model
New gene 4249.1 added to model
New gene 4247.1 added to model
New gene 2954.1 added to model New gene 2954.3 added to model New gene 2954.2 added to model
New gene 2595.1 added to model
New gene 29926.2 added to model New gene 29926.1 added to model New gene 29925.2 added to model New gene 29925.1 added to model
New gene 4351.1 added to model
New gene 56922.1 added to model New gene 64087.1 added to model
New gene 23417.1 added to model
New gene 4357.1 added to model
New gene 130752.1 added to model New gene 4190.1 added to model
New gene 4191.1 added to model
New gene 4200.1 added to model
New gene 4199.1 added to model
New gene 10873.1 added to model
New gene 1557.1 added to model New gene 1543.1 added to model New gene 1545.1 added to model New gene 1544.1 added to model
New gene 4143.1 added to model New gene 27430.2 added to model New gene 4144.1 added to model New gene 27430.1 added to model
New gene 8140.1 added to model
New gene 4548.1 added to model
New gene 4598.1 added to model
New gene 7841.1 added to model
New gene 3635.1 added to model New gene 8867.2 added to model New gene 3636.1 added to model New gene 27124.2 added to model New gene 8867.1 added to model New gene 27124.1 added to model New gene 3633.1 added to model New gene 56623.1 added to model New gene 3632.1 added to model
New gene 3628.1 added to model
New gene 3706.1 added to model New gene 80271.1 added to model New gene 3707.1 added to model
New gene 3612.1 added to model New gene 3613.1 added to model
New gene 51477.1 added to model
New gene 3631.2 added to model New gene 3631.1 added to model New gene 8821.1 added to model
New gene 4121.1 added to model New gene 57134.1 added to model New gene 10905.1 added to model
New gene 11253.1 added to model
New gene 84693.1 added to model
New gene 4594.1 added to model
New gene 4329.1 added to model
New gene 116255.1 added to model New gene 80168.1 added to model
New gene 4507.1 added to model
New gene 100287639.1 added to model New gene 441024.1 added to model
New gene 10797.1 added to model
New gene 56913.1 added to model
New gene 443.1 added to model New gene 91703.1 added to model
New gene 4715.1 added to model New gene 4720.1 added to model New gene 4719.1 added to model New gene 55967.1 added to model New gene 4700.1 added to model New gene 4709.1 added to model New gene 4710.1 added to model New gene 4726.1 added to model New gene 4696.1 added to model New gene 4718.1 added to model New gene 4694.1 added to model New gene 374291.1 added to model New gene 4728.1 added to model New gene 4717.1 added to model New gene 4731.1 added to model New gene 4705.1 added to model New gene 4725.1 added to model New gene 4716.1 added to model New gene 4537.1 added to model New gene 4722.1 added to model New gene 7991.1 added to model New gene 4541.1 added to model New gene 4539.1 added to model New gene 4712.1 added to model New gene 4707.1 added to model New gene 4701.1 added to model New gene 4723.1 added to model New gene 4698.1 added to model New gene 4538.1 added to model New gene 4697.1 added to model New gene 51079.1 added to model New gene 4714.1 added to model New gene 4704.1 added to model New gene 4711.1 added to model New gene 126328.1 added to model New gene 4724.1 added to model New gene 4713.1 added to model New gene 4536.1 added to model New gene 4695.1 added to model New gene 4702.1 added to model New gene 4708.1 added to model New gene 4706.1 added to model New gene 4535.1 added to model New gene 4540.1 added to model New gene 4729.1 added to model New gene 4712.2 added to model New gene 4731.2 added to model New gene 7991.2 added to model
New gene 55191.1 added to model
New gene 4668.1 added to model
New gene 9498.1 added to model New gene 57282.1 added to model
New gene 6528.1 added to model
New gene 481.1 added to model New gene 478.1 added to model New gene 477.1 added to model New gene 23439.1 added to model New gene 483.1 added to model New gene 476.1 added to model New gene 480.1 added to model New gene 482.1 added to model
New gene 389015.1 added to model New gene 6548.1 added to model New gene 6550.1 added to model New gene 6549.1 added to model New gene 6553.1 added to model
New gene 84735.1 added to model
New gene 6559.1 added to model
New gene 123041.2 added to model New gene 57419.1 added to model New gene 9187.1 added to model New gene 123041.3 added to model New gene 25769.1 added to model New gene 123041.1 added to model
New gene 124583.1 added to model
New gene 9583.1 added to model
New gene 4832.1 added to model New gene 10201.1 added to model New gene 4831.1 added to model New gene 4830.1 added to model New gene 29922.2 added to model New gene 4830.2 added to model New gene 29922.1 added to model
New gene 4833.1 added to model
New gene 57127.1 added to model New gene 6005.1 added to model
New gene 6557.1 added to model New gene 6558.1 added to model
New gene 64802.1 added to model
New gene 349565.1 added to model New gene 23057.1 added to model New gene 23057.2 added to model
New gene 4837.1 added to model
New gene 5409.1 added to model
New gene 4846.1 added to model New gene 201288.1 added to model New gene 4842.1 added to model New gene 4843.2 added to model New gene 4843.1 added to model New gene 645740.1 added to model
New gene 55808.1 added to model
New gene 22978.1 added to model
New gene 30833.1 added to model
New gene 93034.2 added to model New gene 93034.1 added to model
New gene 56953.1 added to model
New gene 51251.1 added to model
New gene 4907.1 added to model
New gene 6476.1 added to model
New gene 5009.1 added to model
New gene 5019.1 added to model New gene 64064.1 added to model
New gene 1629.1 added to model New gene 594.1 added to model New gene 593.1 added to model New gene 594.2 added to model
New gene 7372.1 added to model
New gene 26873.1 added to model
New gene 4953.1 added to model
New gene 4942.1 added to model
New gene 1836.1 added to model New gene 10861.1 added to model New gene 10861.3 added to model New gene 10861.2 added to model New gene 1811.1 added to model
New gene 1583.1 added to model
New gene 1584.1 added to model
New gene 1585.1 added to model
New gene 1586.1 added to model
New gene 1588.1 added to model New gene 1588.2 added to model
New gene 1589.1 added to model
New gene 1593.1 added to model
New gene 1553.1 added to model New gene 1548.1 added to model
New gene 1562.1 added to model
New gene 1558.1 added to model New gene 1558.2 added to model
New gene 1559.1 added to model
New gene 1565.1 added to model
New gene 1572.1 added to model
New gene 51302.1 added to model
New gene 1577.1 added to model
New gene 1551.1 added to model
New gene 10858.1 added to model
New gene 66002.1 added to model
New gene 1581.1 added to model
New gene 9420.1 added to model
New gene 1582.1 added to model
New gene 5831.1 added to model New gene 5831.2 added to model
New gene 5051.1 added to model New gene 5049.1 added to model New gene 5050.1 added to model New gene 5048.1 added to model
New gene 7941.1 added to model
New gene 347734.1 added to model
New gene 57194.1 added to model
New gene 5338.1 added to model
New gene 5337.1 added to model
New gene 130013.1 added to model
New gene 5091.1 added to model New gene 5091.2 added to model
New gene 5244.1 added to model New gene 5244.3 added to model New gene 5244.2 added to model
New gene 5139.1 added to model New gene 5142.1 added to model New gene 5151.3 added to model New gene 5153.1 added to model New gene 5150.2 added to model New gene 5143.1 added to model New gene 5150.1 added to model New gene 5137.1 added to model New gene 5144.1 added to model New gene 5136.2 added to model New gene 5140.2 added to model New gene 5151.2 added to model New gene 10846.1 added to model New gene 5151.5 added to model New gene 5140.1 added to model New gene 5141.1 added to model New gene 5138.1 added to model New gene 5136.1 added to model New gene 5151.4 added to model New gene 5151.1 added to model New gene 27115.1 added to model New gene 50940.1 added to model New gene 8622.1 added to model
New gene 5146.1 added to model New gene 5152.17 added to model New gene 5152.6 added to model New gene 5152.11 added to model New gene 5152.2 added to model New gene 8654.2 added to model New gene 5152.10 added to model New gene 5145.1 added to model New gene 5158.1 added to model New gene 5149.1 added to model New gene 5152.12 added to model New gene 5152.15 added to model New gene 5152.5 added to model New gene 5152.20 added to model New gene 5152.19 added to model New gene 5152.16 added to model New gene 8654.3 added to model New gene 5152.14 added to model New gene 5152.13 added to model New gene 5152.7 added to model New gene 5152.3 added to model New gene 8654.1 added to model New gene 5152.18 added to model New gene 5147.1 added to model New gene 5148.1 added to model New gene 5152.4 added to model
New gene 5152.1 added to model
New gene 5161.1 added to model New gene 5162.1 added to model New gene 1737.1 added to model New gene 5160.1 added to model
New gene 55163.1 added to model
New gene 10396.1 added to model
New gene 5105.1 added to model
New gene 5106.1 added to model
New gene 8310.1 added to model
New gene 5833.1 added to model
New gene 10400.2 added to model New gene 10400.1 added to model New gene 10400.3 added to model
New gene 5214.1 added to model New gene 5211.2 added to model New gene 5211.1 added to model New gene 5213.1 added to model
New gene 26227.1 added to model
New gene 5730.1 added to model New gene 27306.1 added to model
New gene 2821.1 added to model
New gene 5740.1 added to model
New gene 5230.1 added to model New gene 375056.1 added to model New gene 5232.1 added to model
New gene 25796.1 added to model
New gene 5236.1 added to model New gene 55276.1 added to model
New gene 9489.1 added to model
New gene 5743.1 added to model New gene 5742.1 added to model
New gene 113235.1 added to model
New gene 5053.1 added to model
New gene 5264.1 added to model
New gene 5728.1 added to model
New gene 8871.1 added to model
New gene 8394.1 added to model New gene 23396.1 added to model New gene 8395.1 added to model
New gene 55361.1 added to model New gene 5297.1 added to model New gene 5298.1 added to model
New gene 5291.1 added to model New gene 5295.3 added to model New gene 5293.1 added to model New gene 8503.1 added to model New gene 5296.1 added to model New gene 5290.1 added to model New gene 5295.1 added to model New gene 5295.2 added to model New gene 10870.1 added to model New gene 5294.1 added to model New gene 23533.1 added to model
New gene 4952.1 added to model New gene 4952.2 added to model
New gene 23236.2 added to model New gene 5336.1 added to model New gene 9651.1 added to model New gene 113026.1 added to model New gene 89869.1 added to model New gene 84812.1 added to model New gene 5330.1 added to model New gene 5335.1 added to model New gene 51196.1 added to model New gene 5333.1 added to model New gene 5332.2 added to model New gene 5331.1 added to model New gene 5335.2 added to model New gene 5334.1 added to model New gene 5332.1 added to model New gene 257068.1 added to model New gene 23236.1 added to model New gene 23007.1 added to model
New gene 5287.1 added to model New gene 5286.1 added to model New gene 5288.1 added to model
New gene 200576.2 added to model New gene 8396.1 added to model New gene 200576.3 added to model New gene 79837.1 added to model New gene 8396.2 added to model New gene 5305.1 added to model New gene 200576.1 added to model
New gene 5289.1 added to model
New gene 10050.1 added to model New gene 10786.1 added to model New gene 10246.1 added to model New gene 6568.1 added to model New gene 6569.1 added to model New gene 10568.1 added to model
New gene 2544.1 added to model
New gene 8398.1 added to model New gene 5320.1 added to model New gene 8398.2 added to model
New gene 5322.1 added to model New gene 5319.1 added to model New gene 81579.1 added to model New gene 64600.1 added to model New gene 26279.1 added to model New gene 8399.1 added to model New gene 30814.1 added to model
New gene 5372.1 added to model New gene 5373.1 added to model
New gene 10654.1 added to model
New gene 79646.1 added to model New gene 80025.2 added to model New gene 53354.1 added to model New gene 53354.3 added to model New gene 80025.1 added to model New gene 53354.2 added to model New gene 80025.3 added to model New gene 80025.4 added to model New gene 55229.1 added to model
New gene 5464.1 added to model
New gene 27068.4 added to model New gene 27068.1 added to model New gene 27068.3 added to model New gene 27068.2 added to model
New gene 8612.1 added to model New gene 8611.1 added to model New gene 8613.1 added to model New gene 8611.2 added to model
New gene 210.1 added to model New gene 210.2 added to model
New gene 60490.1 added to model
New gene 5096.1 added to model New gene 5095.1 added to model
New gene 79717.1 added to model
New gene 5498.1 added to model
New gene 8288.1 added to model
New gene 4353.1 added to model
New gene 5198.1 added to model
New gene 6820.2 added to model
New gene 5625.1 added to model
New gene 58510.1 added to model
New gene 6578.1 added to model
New gene 6580.1 added to model
New gene 221823.2 added to model New gene 5631.1 added to model New gene 221823.1 added to model New gene 5634.1 added to model
New gene 23761.1 added to model
New gene 29968.1 added to model New gene 29968.2 added to model
New gene 8781.1 added to model New gene 5723.1 added to model
New gene 9791.1 added to model
New gene 81490.1 added to model
New gene 10965.1 added to model
New gene 8566.1 added to model
New gene 5315.2 added to model New gene 5313.2 added to model New gene 5315.3 added to model New gene 5313.1 added to model New gene 113452.1 added to model New gene 5315.1 added to model
New gene 7378.2 added to model New gene 7378.1 added to model
New gene 2944.1 added to model New gene 2944.2 added to model
New gene 55312.1 added to model
New gene 5959.1 added to model New gene 8608.1 added to model
New gene 157506.1 added to model New gene 112724.1 added to model New gene 145226.1 added to model New gene 51109.1 added to model New gene 195814.1 added to model New gene 57665.1 added to model New gene 50700.1 added to model
New gene 8228.1 added to model
New gene 6240.1 added to model New gene 6241.1 added to model
New gene 54981.1 added to model
New gene 6120.1 added to model New gene 6120.2 added to model
New gene 22934.1 added to model
New gene 6484.1 added to model New gene 6482.1 added to model New gene 6483.1 added to model New gene 6482.2 added to model
New gene 6487.4 added to model New gene 6487.9 added to model New gene 6487.11 added to model New gene 6487.6 added to model New gene 6487.7 added to model New gene 6487.10 added to model New gene 6487.5 added to model New gene 6487.1 added to model New gene 6487.2 added to model New gene 6487.8 added to model New gene 6487.3 added to model
New gene 6480.1 added to model New gene 6480.3 added to model New gene 6480.2 added to model
New gene 3423.1 added to model New gene 3423.2 added to model
New gene 411.2 added to model New gene 411.1 added to model
New gene 23563.2 added to model New gene 9435.1 added to model New gene 23563.1 added to model New gene 10164.1 added to model New gene 4166.1 added to model
New gene 8534.1 added to model New gene 9469.1 added to model
New gene 2799.1 added to model
New gene 10157.1 added to model
New gene 118881.1 added to model
New gene 3176.1 added to model
New gene 1757.1 added to model
New gene 81537.1 added to model
New gene 6652.1 added to model
New gene 6342.1 added to model
New gene 10993.1 added to model
New gene 9056.1 added to model
New gene 10558.1 added to model New gene 9517.1 added to model
New gene 2098.1 added to model
New gene 8879.1 added to model
New gene 8869.1 added to model
New gene 56848.1 added to model
New gene 55512.1 added to model New gene 55512.2 added to model
New gene 259230.1 added to model
New gene 115111.1 added to model New gene 115019.2 added to model New gene 115111.2 added to model New gene 116369.2 added to model New gene 284129.1 added to model New gene 116369.1 added to model New gene 115019.1 added to model
New gene 26266.1 added to model
New gene 6723.1 added to model
New gene 6647.1 added to model
New gene 6649.1 added to model
New gene 6648.1 added to model
New gene 6611.1 added to model
New gene 6713.1 added to model
New gene 2222.1 added to model
New gene 6715.1 added to model New gene 6716.1 added to model
New gene 6532.1 added to model
New gene 10402.1 added to model
New gene 10610.1 added to model
New gene 256435.1 added to model New gene 30815.1 added to model New gene 81849.1 added to model
New gene 6489.1 added to model
New gene 29906.1 added to model
New gene 412.1 added to model
New gene 6389.1 added to model New gene 6392.1 added to model New gene 6391.1 added to model New gene 6390.1 added to model
New gene 6821.1 added to model
New gene 6888.1 added to model
New gene 6533.1 added to model
New gene 5092.1 added to model New gene 5092.2 added to model
New gene 23530.2 added to model New gene 23530.1 added to model
New gene 10560.1 added to model
New gene 79178.1 added to model
New gene 6567.1 added to model
New gene 7086.1 added to model New gene 84076.1 added to model New gene 8277.1 added to model
New gene 27010.1 added to model
New gene 1890.1 added to model
New gene 7298.1 added to model
New gene 7167.1 added to model New gene 286016.1 added to model
New gene 7296.3 added to model New gene 7296.1 added to model New gene 7296.4 added to model New gene 7296.2 added to model
New gene 114112.1 added to model New gene 10587.1 added to model New gene 10587.3 added to model New gene 10587.2 added to model
New gene 11181.1 added to model
New gene 7166.1 added to model New gene 121278.1 added to model
New gene 6999.1 added to model
New gene 6561.1 added to model
New gene 6916.1 added to model
New gene 7054.1 added to model New gene 7054.3 added to model New gene 7054.2 added to model
New gene 7306.1 added to model
New gene 6898.1 added to model
New gene 2582.1 added to model New gene 2582.2 added to model
New gene 6675.1 added to model New gene 91373.1 added to model
New gene 29880.1 added to model
New gene 7355.1 added to model
New gene 7358.1 added to model
New gene 23169.1 added to model
New gene 5169.1 added to model New gene 5168.1 added to model
New gene 3906.1 added to model
New gene 7357.1 added to model
New gene 11046.1 added to model
New gene 54576.1 added to model
New gene 54575.1 added to model
New gene 7364.1 added to model New gene 54490.1 added to model New gene 7367.1 added to model
New gene 7390.1 added to model
New gene 7389.1 added to model
New gene 131669.1 added to model
New gene 6563.1 added to model New gene 8170.1 added to model
New gene 366.1 added to model
New gene 7498.1 added to model
New gene 9942.1 added to model
New gene 51181.1 added to model
New gene AI990637.1 added to model New gene 64077.1 added to model
New gene 25841.1 added to model
New gene 1356.1 added to model New gene 2495.1 added to model New gene 2509.1 added to model New gene 94033.1 added to model New gene 84343.1 added to model
New gene AV717590.1 added to model New gene 377841.1 added to model
New gene AA532636.1 added to model
New gene 285973.1 added to model New gene D29675.1 added to model New gene NOS2A.1 added to model
New gene AI769281.1 added to model New gene 57786.1 added to model
New gene AI971036.1 added to model
New gene 56954.1 added to model
New gene 2643.1 added to model
New gene H77542.1 added to model
New gene LOC374569.1 added to model
New gene AI222095.1 added to model New gene AI697028.1 added to model New gene D87002.1 added to model New gene 728441.1 added to model New gene 2686.1 added to model New gene 728226.1 added to model New gene NM_013421.1 added to model
New gene AA502753.1 added to model
New gene 3704.1 added to model
New gene AI656480.1 added to model New gene BE042354.1 added to model
New gene U37519.1 added to model
New gene 7915.1 added to model New gene 9856.1 added to model
New gene AI640625.1 added to model
New gene 79611.1 added to model
New gene HG2846-HT2983.1 added to model
New gene 125061.1 added to model
New gene 54.1 added to model New gene 51205.1 added to model New gene 55.1 added to model New gene AI191472.1 added to model New gene 248.1 added to model New gene 249.1 added to model New gene 250.1 added to model New gene 251.1 added to model
New gene AA676725.1 added to model New gene 196951.1 added to model
New gene 10449.1 added to model New gene 4645.1 added to model
New gene AI761708.1 added to model
New gene AA664770.1 added to model New gene AI684467.1 added to model
New gene 122970.1 added to model New gene 11332.1 added to model New gene 80864.1 added to model New gene 83715.1 added to model New gene 5538.1 added to model New gene 9374.1 added to model New gene R33828.1 added to model
New gene AA526438.1 added to model New gene H17063.1 added to model New gene 51102.1 added to model New gene 55825.1 added to model
New gene 33.1 added to model New gene 37.1 added to model New gene AI285872.1 added to model
New gene AA788780.1 added to model New gene AA977580.1 added to model New gene 23305.1 added to model New gene AI694761.1 added to model New gene AI915649.1 added to model New gene AL525798.1 added to model New gene AV727634.1 added to model New gene 728637.1 added to model New gene LOC728997.1 added to model
New gene AA278423.1 added to model
New gene R39999.1 added to model
New gene AI653169.1 added to model New gene 206.1 added to model New gene AW277253.1 added to model
New gene 55753.1 added to model
New gene 641649.1 added to model
New gene AI934540.1 added to model New gene W74642.1 added to model
New gene AI824319.1 added to model
New gene AI469183.1 added to model New gene BC005314.1 added to model New gene BF195998.1 added to model
New gene AA614647.1 added to model
New gene NM_001929.1 added to model
New gene AI090874.1 added to model New gene AL048840.1 added to model New gene BG035985.1 added to model
New gene BE966236.1 added to model New gene 50484.1 added to model
New gene 3156.1 added to model
New gene AA629629.1 added to model New gene AA854479.1 added to model New gene AI345944.1 added to model New gene AI378339.1 added to model New gene AI601100.1 added to model New gene AI631997.1 added to model New gene AI935189.1 added to model New gene 124454.1 added to model New gene F23536.1 added to model New gene FLJ44968.1 added to model New gene H45672.1 added to model New gene H53099.1 added to model New gene 3550.1 added to model New gene LOC727762.1 added to model New gene 56901.1 added to model New gene 54539.1 added to model
New gene AF080579.1 added to model New gene AI348006.1 added to model New gene 642502.1 added to model
New gene AF116616.1 added to model New gene PRO1933.1 added to model New gene 79966.1 added to model
New gene 400410.1 added to model
New gene AA021081.1 added to model New gene AI440329.1 added to model New gene R06874.1 added to model New gene 54963.1 added to model
New gene 84890.1 added to model New gene AV713053.1 added to model
New gene AD000092.1 added to model
New gene AW299740.1 added to model New gene J03866.1 added to model
New gene C7orf24.1 added to model
New gene AI926493.1 added to model New gene 83594.1 added to model
New gene 26275.1 added to model
New gene 10637.1 added to model New gene 29920.1 added to model New gene 65263.1 added to model
New gene AI539321.1 added to model New gene 23475.1 added to model
New gene 6173.1 added to model
New gene AI373818.1 added to model
New gene 10005.1 added to model
New gene R14373.1 added to model
New gene AI435857.1 added to model
New gene 6697.1 added to model
New gene 5805.1 added to model
New gene AA177072.1 added to model New gene 54995.1 added to model
New gene AI924226.1 added to model New gene 100128062.1 added to model
New gene AI291895.1 added to model New gene M68895.1 added to model New gene X63359.1 added to model
New gene 1595.1 added to model New gene 83530.1 added to model
New gene AA419122.1 added to model New gene AA576959.1 added to model New gene 8776.1 added to model New gene 8898.1 added to model New gene 9107.1 added to model New gene 29085.1 added to model New gene 130367.1 added to model New gene 23517.1 added to model New gene 51095.1 added to model
New gene AA203143.1 added to model New gene AGPAT7.1 added to model New gene AI818585.1 added to model New gene AI971023.1 added to model New gene 1956.1 added to model New gene 54898.1 added to model New gene 60481.1 added to model New gene 79071.1 added to model New gene 114799.1 added to model New gene 157570.1 added to model New gene 8372.1 added to model New gene LOC647190.1 added to model New gene 9926.1 added to model New gene 129642.1 added to model New gene MBOAT5.1 added to model New gene 79143.1 added to model New gene N63787.1 added to model New gene 80339.1 added to model New gene 6901.1 added to model New gene W87865.1 added to model
New gene AI024818.1 added to model New gene AI091231.1 added to model New gene AI480132.1 added to model New gene AI972237.1 added to model New gene AL050025.1 added to model New gene 763.1 added to model New gene 11238.1 added to model New gene 765.1 added to model New gene 767.1 added to model New gene 8883.1 added to model New gene R51273.1 added to model
New gene AL038231.1 added to model
New gene 215.1 added to model New gene U52111.1 added to model
New gene 641372.1 added to model New gene 641371.1 added to model
New gene 9045.1 added to model
New gene 4017.1 added to model
New gene 4025.1 added to model
New gene 84105.1 added to model
New gene 25830.1 added to model
New gene 84569.1 added to model
New gene 59272.1 added to model
New gene 93492.1 added to model
New gene 1632.1 added to model New gene 10455.1 added to model
New gene 7263.1 added to model
New gene 1267.1 added to model
New gene 54658.1 added to model
New gene 1215.1 added to model
New gene 1357.1 added to model New gene 1358.1 added to model New gene 57094.1 added to model New gene 93979.1 added to model
New gene 7177.1 added to model New gene 64499.1 added to model New gene 23430.1 added to model
New gene 1636.1 added to model
New gene 9365.1 added to model
New gene 9331.1 added to model
New gene 26063.1 added to model
New gene 1891.1 added to model
New gene 1666.1 added to model
New gene 8529.1 added to model New gene 4051.1 added to model New gene 126410.1 added to model
New gene 64834.1 added to model
New gene 8897.1 added to model New gene 8897.3 added to model New gene 8897.2 added to model
New gene 2880.1 added to model New gene 2882.1 added to model
New gene 284111.1 added to model
New gene 9152.1 added to model
New gene 9497.1 added to model
New gene 115584.1 added to model
New gene 6574.1 added to model New gene 6575.1 added to model
New gene 142680.1 added to model
New gene 6534.1 added to model
New gene 3293.1 added to model
New gene 1351.1 added to model New gene 1347.1 added to model New gene 1329.1 added to model New gene 1327.1 added to model New gene 341947.1 added to model New gene 9167.1 added to model New gene 1350.1 added to model New gene 4512.1 added to model New gene 1349.1 added to model New gene 1339.1 added to model New gene 1345.1 added to model New gene 4513.1 added to model New gene 9377.1 added to model New gene 125965.1 added to model New gene 4514.1 added to model New gene 170712.1 added to model New gene 1346.1 added to model New gene 1340.1 added to model New gene 84701.1 added to model New gene 1337.1 added to model
New gene 1622.1 added to model
New gene 225.1 added to model
New gene 28965.1 added to model
New gene 23205.1 added to model New gene 81616.1 added to model
New gene 26061.1 added to model
New gene 5825.1 added to model
New gene 54716.1 added to model New gene 57393.1 added to model
New gene 55748.1 added to model
New gene 6564.1 added to model
New gene 2694.1 added to model New gene 8029.1 added to model New gene 81693.1 added to model
New gene 1800.1 added to model
New gene 5184.1 added to model
New gene 1200.1 added to model
New gene 2168.1 added to model
New gene 51056.1 added to model
New gene 9390.1 added to model
New gene 55065.1 added to model
New gene 1594.1 added to model
New gene 8435.1 added to model New gene 6646.1 added to model
New gene 3988.1 added to model
New gene 4891.1 added to model
New gene 30061.1 added to model
New gene 9843.1 added to model
New gene 4524.1 added to model
Save the resulting model.
save('SubNetworkRecon.mat', 'modelConsistent')
Size of the original Recon model:
[nMet,nRxn] = size(model.S);
fprintf('%6s\t%6s\n','#mets','#rxns'); fprintf('%6u\t%6u\t%s%s\n',nMet,nRxn,' total in Recon')
#mets #rxns 5063 7440 total in Recon
Size of the resulting Recon subnetwork:
[nMet,nRxn] = size(modelConsistent.S);
fprintf('%6s\t%6s\n','#mets','#rxns'); fprintf('%6u\t%6u\t%s%s\n',nMet,nRxn,' total in Recon subnetwork')
#mets #rxns 2910 5245 total in Recon subnetwork
Consider to evaluate the resulting model with the tutorial modelProperties and modelSanityChecks to ensure proper functioning of the generic subnetwork of Recon.

References

[1] Brunk, E. et al. Recon 3D: A resource enabling a three-dimensional view of gene variation in human metabolism. (submitted) 2017.
[2] Thiele I., Swainston N., Fleming R.M.T., et al. (2013) A community-driven global reconstruction of human metabolism. Nat. Biotechnol., 31, 419–425.
[3] Mardinoglu A., Agren R., Kampf C., et al. (2014) Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat. commun., 5, 3083.
[4] Sahoo S, Haraldsdóttir HS, Fleming RM, Thiele I. Modeling the effects of commonly used drugs on human metabolism. FEBS J. 2015 Jan;282(2):297-317.
[5] Vlassis N, Pacheco MP, Sauter T. Fast reconstruction of compact context-specific metabolic network models. PLoS Comput Biol. 2014 Jan;10(1).