Gene expression and evaluation system using a filter table with a gene expression database

• US 6,532,462 B2
• Filed: 08/27/2001
• Issued: 03/11/2003
• Est. Priority Date: 07/25/1997
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Balaban, David J.
• Primary Examiner(s): CHOULES, JACK M
• Application Number:
  US09/940,285
• Publication Number:
  US 20020062319A1
• Time in Patent Office: 561 Days
• Field of Search: 435/6, 702/19, 702/20, 707/3, 707/4, 707/5, 707/6, 707/104
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: H04M 1/006 Call diverting means
• CPC Class Codes: H04M 1/724 User interfaces specially adapted for cordless or mobile telephones
• CPC Class Codes: H04M 2207/206 composed of PSTN and wireless network
• CPC Class Codes: H04M 3/46 Arrangements for calling a number of substations in a predetermined sequence until an answer is obtained
• CPC Class Codes: H04M 3/54 Arrangements for diverting calls for one subscriber to another predetermined subscriber based on the calling party profile H04M3/42059; based on location H04M3/42348; based on presence H04M3/42365; to voice mail H04M3/53308
• CPC Class Codes: Y10S 128/922 including image analysis
• CPC Class Codes: Y10S 707/925 Drafting an application
• CPC Class Codes: Y10S 707/955 Object-oriented
• CPC Class Codes: Y10S 707/99933 Query processing, i.e. searching
• CPC Class Codes: Y10S 707/99934 Query formulation, input preparation, or translation
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

A filter table provides a framework in which queries are efficiently and easily developed to access a gene expression database. The filter table is used to filter a plurality of expression levels to return a reduced set of expression levels, which may be further queried to provide more specific results. Using the filtering and querying provided 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.

Claims

1. In a computer system, a method for operating a database storing expression level information comprising:

providing a database comprising expression levels for each of a plurality of genes or expressed sequence tags (EST) as measured in each of a plurality of tissue types;

filtering a plurality of expression levels to obtain a reduced set of expression levels, wherein the step of filtering includes substeps of

allowing a user to define a filter table in row and column correspondence to a target table; and

applying the filter table to the target table to obtain the reduced set of expression levels;

accepting a user query to said reduced set of expression levels 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 levels stored in said database to identify said desired genes or EST.

2. The method of claim 1 further comprising:

displaying information identifying said desired genes or EST.

3. The method of claim 1 wherein said plurality of tissue types comprise a diseased tissue type.

4. The method of claim 1 wherein said plurality of tissue types comprise a healthy tissue type.

5. The method of claim 1 wherein said plurality of tissue types comprise a cancerous tissue type.

6. The method of claim 1 wherein said plurality of tissue types comprise a drug treated tissue type.

7. The method of claim 1 wherein said plurality of tissue types comprise issues obtained from disparate species.

8. The method of claim 1 wherein said plurality of tissue types comprise tissues obtained from disparate organs.

9. The method of claim 1 wherein said expression level characteristics comprise expression level ranges as measured for a particular gene in at least two of said plurality of tissue types.

10. The method of claim 1 wherein said expression level characteristics comprise relationships among expression levels as measured for a particular gene in at least two of said plurality of tissue types.

11. The method of claim 1 further comprising:

accepting user input selecting two of said plurality tissue types for graphical display;

displaying a first axis corresponding to a first one of said two tissue types;

displaying a second axis corresponding to a second one of said two tissue types;

for a selected one of said plurality of genes or EST, displaying a mark at a position wherein said position is selected relative to said first axis in accordance with an expression level of said selected gene or EST measured in said first tissue type and selected relative to said second axis in accordance with an expression level of said selected gene or EST measured in said second tissue type.

12. The method of claim 11 further comprising:

repeating said operation of displaying a mark for a plurality of selected genes or EST.

13. In a computer system, a method for operating a database storing information about compound concentration comprising:

providing a database comprising concentrations of a plurality of compounds as measured in a plurality of samples;

filtering a plurality of expression levels to obtain a reduced set of expression levels, wherein the step of filtering includes substeps of

allowing a user to define a filter table in row and column correspondence to a target table; and

applying the filter table to the target table to obtain the reduced set of expression levels;

accepting a user query to said reduced set of expression levels to identify desired ones of said plurality of compounds, said user query specifying concentration characteristics of said desired compounds in selected ones of said plurality of samples; and

comparing said concentration characteristics to said concentrations stored in said database to identify said desired compounds.

14. A computer program product for operating a database storing expression level information comprising:

code that provides a database comprising expression levels for each of a plurality of genes or expressed sequence tags (EST) as measured in each of a plurality of tissue types;

code that filters a plurality of expression levels to obtain a reduced set of expression levels, wherein the step of filtering includes substeps of

allowing a user to define a filter table in row and column correspondence to a target table; and

applying the filter table to the target table to obtain the reduced set of expression levels;

code that accepts a user query to said reduced set of expression levels 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 levels stored in said database to identify said desired genes or EST; and

a computer-readable storage medium for storing the codes.

15. The product of claim 14 further comprising:

code that displays information identifying said desired genes or EST.

16. The product of claim 14 wherein said plurality of tissue types comprise a diseased tissue type.

17. The product of claim 14 wherein said plurality of tissue types comprise a healthy tissue type.

18. The product of claim 14 wherein said plurality of tissue types comprise a cancerous tissue type.

19. The product of claim 14 wherein said plurality of tissue types comprise a drug treated tissue type.

20. The product of claim 14 wherein said plurality of tissue types comprise tissues obtained from disparate species.