Human metabolic models and methods
First Claim
1. A computer readable medium or media, comprising:
- (a) a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product, wherein at least one of said Homo sapiens reactions is annotated to indicate an associated gene;
(b) a gene database comprising information characterizing said associated gene;
(c) a constraint set for said plurality of Homo sapiens reactions, and (d) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said data representation, wherein said at least one flux distribution is predictive of a Homo sapiens physiological function.
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Abstract
The invention provides in silico models for determining the physiological function of human cells, including human skeletal muscle cells. The models include a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, a constraint set for the plurality of Homo sapiens reactions, and commands for determining a distribution of flux through the reactions that is predictive of a Homo sapiens physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated Homo sapiens reaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silico Homo sapiens model and methods for determining a Homo sapiens physiological function using a model of the invention.
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Citations
66 Claims
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1. A computer readable medium or media, comprising:
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(a) a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product, wherein at least one of said Homo sapiens reactions is annotated to indicate an associated gene;
(b) a gene database comprising information characterizing said associated gene;
(c) a constraint set for said plurality of Homo sapiens reactions, and (d) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said data representation, wherein said at least one flux distribution is predictive of a Homo sapiens physiological function. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A computer readable medium or media, comprising:
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(a) a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product, wherein at least one of said Homo sapiens reactions is a regulated reaction;
(b) a constraint set for said plurality of Homo sapiens reactions, wherein said constraint set includes a variable constraint for said regulated reaction, and (c) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said data representation, wherein said at least one flux distribution is predictive of a Homo sapiens physiological function. - View Dependent Claims (14, 15, 16, 17, 18, 19)
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20. A computer readable medium or media, comprising:
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(a) a data structure relating a plurality of Homo sapiens skeletal muscle cell reactants to a plurality of Homo sapiens skeletal muscle cell reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
(b) a constraint set for said plurality of Homo sapiens reactions, and (c) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said data representation, wherein said at least one flux distribution is predictive of Homo sapiens skeletal muscle cell energy production.
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21. A method for predicting a Homo sapiens physiological function, comprising:
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(a) providing a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product, wherein at least one of said Homo sapiens reactions is annotated to indicate an associated gene;
(b) providing a constraint set for said plurality of Homo sapiens reactions;
(c) providing an objective function, and (d) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby predicting a Homo sapiens physiological function related to said gene. - View Dependent Claims (22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44)
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45. A method for predicting a Homo sapiens physiological function, comprising:
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(a) providing a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product, wherein at least one of said Homo sapiens reactions is a regulated reaction;
(b) providing a constraint set for said plurality of Homo sapiens reactions, wherein said constraint set includes a variable constraint for said regulated reaction;
(c) providing a condition-dependent value to said variable constraint;
(d) providing an objective function, and (e) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby predicting a Homo sapiens physiological function. - View Dependent Claims (46, 47, 48, 49, 50, 51)
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52. A method for predicting Homo sapiens growth, comprising:
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(a) providing a data structure relating a plurality of Homo sapiens skeletal muscle cell reactants to a plurality of Homo sapiens skeletal muscle cell reactions, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
(b) providing a constraint set for said plurality of Homo sapiens reactions;
(c) providing an objective function, and (d) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby predicting Homo sapiens skeletal muscle cell energy production.
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53. A method for making a data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions in a computer readable medium or media, comprising:
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(a) identifying a plurality of Homo sapiens reactions and a plurality of Homo sapiens reactants that are substrates and products of said Homo sapiens reactions;
(b) relating said plurality of Homo sapiens reactants to said plurality of Homo sapiens reactions in, a data structure, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
(c) determining a constraint set for said plurality of Homo sapiens reactions;
(d) providing an objective function;
(e) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, and (f) if said at least one flux distribution is not predictive of a Homo sapiens physiological function, then adding a reaction to or deleting a reaction from said data structure and repeating step (e), if said at least one flux distribution is predictive of a Homo sapiens physiological function, then storing said data structure in a computer readable medium or media. - View Dependent Claims (54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65)
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66. A data structure relating a plurality of Homo sapiens reactants to a plurality of Homo sapiens reactions, wherein said data structure is produced by a process comprising:
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(a) identifying a plurality of Homo sapiens reactions and a plurality of Homo sapiens reactants that are substrates and products of said Homo sapiens reactions;
(b) relating said plurality of Homo sapiens reactants to said plurality of Homo sapiens reactions in a data structure, wherein each of said Homo sapiens reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
(c) determining a constraint set for said plurality of Homo sapiens reactions;
(d) providing an objective function;
(e) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, and (f) if said at least one flux distribution is not predictive of Homo sapiens physiology, then adding a reaction to or deleting a reaction from said data structure and repeating step (e), if said at least one flux distribution is predictive of Homo sapiens physiology, then storing said data structure in a computer readable medium or media.
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Specification