System reconstruction: integrative analysis of biological data
AssigneeGenego, Inc.
InventorsTatiang Nikolskaya, Andrei Bugrim, Alexander Markov, Evgeny Kirttlov, Igor Garley
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Abstract
The process of System Reconstruction is used to integrate sequence data, clinical data, experimental data, and literature into functional models of disease pathways. System Reconstruction models serve as informational “skeletons” for integrating various types of “high throughput” data. The present invention provides the first metabolic reconstruction study of a eukaryotic organism based solely on expressed sequence tag (EST) data.
Claims9
A method for reconstructing metabolism of an organism based on expressed sequence tag data.
A method for reconstructing metabolism of an organism comprising:
- (a) collecting data regarding the organism's metabolism;
- (b) linking the data into metabolic pathways;
- (c) identifying interconnections between the metabolic pathways;
- (d) creating a map of the organism's metabolism by integrating information obtain in steps (a), (b), and (c).
A method for identifying drug targets comprising:
- (a) collecting data regarding an organism's metabolism for both non-disease and disease states;
- (b) linking the data into metabolic pathways;
- (c) identifying interconnections between the metabolic pathways;
- (d) creating a map of the organism's metabolism by integrating information obtain in steps (a), (b), and (c).
- (e) identifying drug targets by comparing differences between non-disease and disease states using the map.
A method for identifying targets for gene therapy comprising:
- (a) collecting data regarding an organism's metabolism for a first developmental state and a second developmental state;
- (b) linking the data into metabolic pathways;
- (c) identifying interconnections between the metabolic pathways;
- (d) creating a map of the organism's metabolism by integrating information obtain in steps (a), (b), and (c).
- (e) identifying targets for gene therapy by comparing differences between the first developmental state and the second developmental state using the map.
A method for identifying interconnections between biological processes of an organism comprising:
- (a) collecting data regarding the organism's biological processes, including inputs and outputs of the processes;
- (b) linking the data into pathways based on shared inputs and outputs;
- (c) identifying interconnections between the pathways;
- (d) creating a map of the organism's biological processes by integrating information obtain in steps (a), (b), and (c).
Dependencies are inferred from the claim text.