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US 2011/0213603 A1Published application
Compositions and methods for modeling human metabolism
AssigneeThe Regents of the University of California
InventorsBernard O. Palsson, Natalie Duarte, Scott Becker, Neema Jamshidi
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Abstract
The present invention provides Homo sapiens Recon 1, a manually assembled, functionally validated, bottom-up reconstruction of human metabolism. Recon 1's 1496 genes, 2004 proteins, 2766 metabolites, and 3311 biochemical and transport reactions were extracted from more than 50 years of legacy biochemical knowledge and Build 35 of the human genome sequence.
Claims39
A computer readable medium comprising:
- (a) a data structure relating a plurality of H. sapiens reactants to a plurality of H. sapiens reactions, wherein each of the H. sapiens reactions comprises one or more reactants identified as a substrate of the reaction, one or more reactants identified as a product of the reaction, and a stoichiometric coefficient relating the substrate and the product, wherein at least one of the H. sapiens reactions is annotated to indicate an associated gene in Table 4;
- (b) a gene database comprising information characterizing the associated gene;
- (c) a constraint set for the plurality of H. sapiens reactions;
- and
- (d) commands for determining at least one flux distribution that minimizes or maximizes an objective function when the constraint set is applied to the data structure, wherein the at least one flux distribution is predictive of a H. sapiens physiological function,
- wherein the data structure comprises Tables 1, 4, 5, 7 and 8.
3 more elements
A computer readable medium comprising:
- (a) a data structure relating a plurality of H. sapiens reactants to a plurality of H. sapiens reactions, wherein each of the H. sapiens reactions comprises one or more reactants identified as a substrate of the reaction, one or more reactants identified as a product of the reaction and a stoichiometric coefficient relating the substrate and the product;
- (b) a constraint set for the plurality of H. sapiens reactions;
- and
- (c) commands for determining at least one flux distribution that minimizes or maximizes an objective function when the constraint set is applied to the data representation, wherein the at least one flux distribution is predictive of H. sapiens cellular growth,
- wherein the data structure comprises Tables 1, 4, 5, 7 and 8.
2 more elements
A method for predicting a H. sapiens physiological function comprising:
- (a) providing a data structure relating a plurality of H. sapiens reactants to a plurality of reactions, wherein each of the H. sapiens reactions comprises one or more reactants identified as a substrate of the reaction, one or more reactants identified as a product of the reaction and a stoichiometric coefficient relating the substrate and the product;
- (b) providing a constraint set for the plurality of H. sapiens reactions;
- (c) providing an objective function;
- and
- (d) determining at least one flux distribution that minimizes or maximizes the objective function when the constraint set is applied to the data structure, thereby predicting a H. sapiens physiological function related to the gene, wherein the data structure comprises Tables 1, 4, 5, 7 and 8.
2 more elements
A method for predicting human cellular growth comprising:
- (a) providing a data structure relating a plurality of H. sapiens reactants to a plurality of H. sapiens reactions, wherein each of the H. sapiens reactions comprises one or more reactants identified as a substrate of the reaction, one or more reactants identified as a product of the reaction and a stoichiometric coefficient relating the substrate and the product;
- (b) providing a constraint set for the plurality of H. sapiens reactions;
- (c) providing an objective function;
- and
- (d) determining at least one flux distribution that minimizes or maximizes the objective function when the constraint set is applied to the data structure, thereby predicting human cellular growth,
- wherein the data structure comprises Tables 1, 4, 5, 7 and 8.
3 more elements
Dependencies are inferred from the claim text.