Methods for identification of novel protein drug targets and biomarkers utilizing functional networks

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. System Reconstruction also provides a method for the identification of novel therapeutic targets and biomarkers using network analysis. The initial seed networks are built from the lists of novel targets for diseases with the high-throughput experimental data being superimposed on the seed networks to identify specific targets.

What is claimed is: 
     
         1 . A method for identifying drug or gene therapy 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 the interconnections between the metabolic pathways;   d) creating a map of the organism's metabolism by integrating information obtained in a), b) and c); and   e) identifying drug targets by comparing differences between non-disease and disease states using the map.