Gene expression and evaluation system
AssigneeAffymetrix, Inc.
InventorDavid J. Balaban
Life of this patent
Estimating the term…
Abstract
An efficient and easy to use query system for a gene expression database. Using such a system, one can easily identify genes or expressed sequence tags whose expression correlates to particular tissue types. Various tissue types may correspond to different diseases, states of disease progression, different organs, different species, etc. Researchers may now use large scale gene expression databases to full advantage.
Claims25
In a computer system, a method for operating a database storing expression level information comprising:
- providing a database comprising files of expression level results for each of a plurality of genes or expressed sequence tags (EST) as measured in each of a plurality of tissue types, each file representing one experiment;
- normalizing the expression level results in selected files relative to a known expression level of a housekeeping gene and/or according to an average value of expression level results for all genes in the file;
- accepting a user query to said database to identify desired ones of said plurality of genes or EST, said user query specifying expression level characteristics of said desired genes;
- and
- comparing said expression level characteristics to said expression level results stored in said database to identify said desired genes or EST.
A computer program product for operating a database storing expression level information comprising:
- code that provides a database a database comprising files of expression level results for each of a plurality of genes or expressed sequence tags (EST) as measured in each of a plurality of tissue types, each file representing one experiment;
- code that normalizes the expression level results in selected files relative to a known expression level of a housekeeping gene and/or according to an average value of expression level results for all genes in the file;
- code that accepts a user query to said database to identify desired ones of said plurality of genes or EST, said user query specifying expression level characteristics of said desired genes;
- code that compares said expression level characteristics to said expression level results stored in said database to identify said desired genes or EST;
- and
- a computer-readable storage medium for storing the codes.
A computer system comprising:
- a processor;
- and
- a memory storing code to operate said processor, said code comprising:
- code that provides a database a database comprising files of expression level results for each of a plurality of genes or expressed sequence tags (EST) as measured in each of a plurality of tissue types, each file representing one experiment;
- codes that normalizes the expression level results in selected files relative to a known expression level of a housekeeping gene and/or according to an average value of expression level results for all genes in the file;
- code that accepts a user query to said database to identify desired ones of said plurality of genes or EST, said user query specifying expression level characteristics of said desired genes;
- and
- code that compares said expression level characteristics to said expression level results stored in said database to identify said desired genes or EST.
Dependencies are inferred from the claim text.