Patent ID: 7020561

Claim:
A method of analyzing gene expression data comprising: providing a data warehouse comprising a plurality of databases for storing data including quantitative gene expression data obtained from microarray analysis of gene fragments, sample data corresponding to tissues or cell lines from which the gene fragments were derived, and gene annotation data corresponding to the gene fragments for uniquely identifying the gene expression data; providing an analysis engine for analysis of data in the data warehouse; providing a user interface for submitting search queries to the analysis engine and for receiving search results; receiving a first search query comprising a first sample set; correlating the first search query with its corresponding gene expression data; performing a first gene signature analysis to identify gene fragments that have gene expression responses within at least one user-specified threshold; receiving a second search query comprising a second sample set; correlating the second search query with its corresponding gene expression data; performing a second gene signature analysis to identify gene fragments that have gene expression responses within the at least one user-specified threshold; and performing a gene signature differential analysis by comparing the first and second gene signature analyses to identify at least two sets of differentially expressed gene fragments; wherein the at least one user-specified threshold comprises a selected percentage of a total number of samples in each sample set.