Method and apparatus for providing an expression data mining database

• US 6,687,692 B1
• Filed: 11/02/2000
• Issued: 02/03/2004
• Est. Priority Date: 09/17/1998
• 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., Khurgin, Elina
• Primary Examiner(s): Amsbury, Wayne
• Application Number:
  US09/705,335
• Time in Patent Office: 1,188 Days
• Field of Search: 707/6, 702/20
• US Class Current: 1/1
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: G06F 16/972 Access to data in other repository systems, e.g. legacy data or dynamic Web page generation
• CPC Class Codes: G06F 2216/03 Data mining
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: Y10S 707/99936 Pattern matching access

Abstract

According to the invention, a system and method for organizing expression information in a way that facilitates data mining. A database model is provided which may organize information relating to, e.g., sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results. The model is readily translatable into database languages such as SQL and the like. The database model scales to permit mining of expression or concentration information collected from large numbers of samples.

Claims

1. A computer based method for mining a plurality of experiment information for a pattern, said method comprising:

collecting information from experiments and chip designs;

selecting from said experiments and said chip designs ones to be mined;

defining at least one of a plurality of groupings for said experiments to be mined;

selecting based upon said at least one of a plurality of groupings, information about said plurality of experiments to be mined, forming a plurality of resulting information, said plurality of resulting information including at least a resulting gene set; and

formatting said plurality of resulting information for viewing by a user.

2. The method of claim 1 wherein experiments to be mined are selected based upon at least one of a plurality of experimental analyses.

3. The method of claim 1 wherein said at least one of a plurality of groupings is a sample type.

4. The method of claim 1 wherein said at least one of a plurality of groupings is a sample attribute.

5. The method of claim 1 wherein said plurality of groupings are sample attributes having a non-hierarchical arrangement.

6. The method of claim 1 further comprising adding experiments to said experiments to be mined.

7. The method of claim 1 further comprising deleting experiments to said experiments to be mined.

8. The method of claim 1 wherein said pattern is a gene pathway.

9. The method of claim 1 wherein said pattern is a drug toxicity.

10. The method of claim 1 further comprising enabling a user to apply set theory operations on said resulting gene sets.

11. A computer based method for working with expression information, said method comprising:

collecting information about a plurality of results of a plurality of experiments;

gathering information about samples and information about said plurality of experiments;

adding at least one of a plurality of attributes to said information about said plurality of experiments;

transforming said plurality of results of experiments, to form a plurality of transformed information;

mining said plurality of transformed information; and

visualizing said plurality of transformed information.

12. The method of claim 11 wherein said information about said plurality of experiments comprises at least one of a plurality of experimental analyses.

13. The method of claim 12 wherein said at least one of a plurality of experimental analyses comprises one or more experimental analyses.

14. The method of claim 11 wherein said transforming comprises normalizing and said transformed information comprises normalized information.

15. The method of claim 11 further comprising recording one or more results of said mining said plurality of transformed information.

16. The method of claim 11 further comprising citing theories about said transformed information.

17. A computer program product for mining a plurality of experiment information for a pattern, said computer program product comprising:

code for collecting information from experiments and chip designs;

code for selecting a subset of said experiments and said chip designs, said subset being a plurality of experiments to be mined;

code for defining at least one of a plurality of groupings for said experiments to be mined;

code for selecting based upon said at least one of a plurality of groupings, information about said plurality of experiments to be mined, to form a plurality of resulting information, said plurality of resulting information including at least a resulting gene set;

code for formatting said plurality of resulting information for viewing by a user; and

a computer readable storage medium for containing the codes.

18. The program product of claim 17 wherein said at least one of a plurality of groupings is a sample type.

19. The computer program product of claim 17 wherein said at least one of a plurality of groupings is a sample attribute.

20. The computer program product of claim 17 wherein said plurality of groupings are sample attributes having a non-hierarchical arrangement.

21. The computer program product of claim 17 further comprising code for adding experiments to said experiments to be mined.

22. The computer program product of claim 17 further comprising code for deleting experiments to said experiments to be mined.

23. The computer program product of claim 17 wherein said pattern is a gene pathway.

24. The computer program product of claim 17 wherein said pattern is a drug toxicity.

25. The computer program product of claim 17 further comprising code for enabling a user to apply set theory operations on said resulting gene sets.

26. A computer program product for working with expression information, said computer program product comprising:

code for collecting information about a plurality of results of a plurality of experiments;

code for gathering information about samples and information about said plurality of experiments;

code for adding at least one of a plurality of attributes to said information about said plurality of experiments;

code for transforming said plurality of results of experiments, to form a plurality of transformed information;

code for mining said plurality of transformed information;

code for visualizing said plurality of transformed information; and

a computer readable storage medium for storing the codes.

27. The computer program product of claim 26 further comprising code for citing theories about said transformed information.

28. The computer program product of claim 26 wherein said code for transforming further comprises code for normalizing and said transformed information further comprises normalized information.

29. A system for managing expression information comprising:

a database;

a computer memory; and

a processor, said processor operatively disposed to;

collect information about a plurality of results of a plurality of experiments;

gather information about samples and information about said plurality of experiments;

add at least one of a plurality of attributes to said information about said plurality of experiments;

transform said plurality of results of experiments, to form a plurality of transformed information;

mine said plurality of transformed information; and

visualize said plurality of transformed information.