Patent ID: 7251642

Claim:
A platform comprising a processor executing a program for analyzing gene expression data, wherein the platform comprising: a data warehouse comprising a plurality of databases for storing gene expression data, sample data that corresponds to the gene expression data, and gene index data that identifies the gene expression data, wherein the plurality of databases are integrated into a relational database having a relational database management system for managing data flow to and from the data warehouse; a run time engine receiving gene expression data from the data warehouse by means of the relational database management system; storing the received gene expression data in the form of core and derived gene expression data arranged in a matrix of absent/present calls and intensities or expression values for each sample/gene pair in memory mapped files in a workspace file system; wherein the run time engine comprising a plurality of analysis tools that accesses and analyzes the core and derived gene expression data in the memory mapped files in the workspace file system using a low level code, without directly accessing the relational database management system; a matrix manager disposed between the data warehouse and the run time engine copying and refreshing the core and derived data into the matrix by creating a union of matrices from two sets of data; a first application programming interface for accessing gene expression data, the first interface comprising a low-level interface providing direct access to individual core and derived gene expression data in the memory mapped files; a user interface to the plurality of analysis tools for entry of analysis queries and output of query responses; a second application programming interface coupled between the user interface and the first application programming interface transferring analysis queries to the first application programming interface, wherein the second application programming interface comprises a high-level interface to the run time engine; and a display outputting one or more gene signatures, gene signature graphs, fold change, and ENortherns generated from the analysis of core and derived gene expression data from the run time engine.