Integrated system for gene expression analysis

• US 20030009294A1
• Filed: 12/20/2001
• Published: 01/09/2003
• Est. Priority Date: 06/07/2001
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Cheng, Jill
• Application Number:
  US10/026,110
• Publication Number:
  US 20030009294A1
• Time in Patent Office: Days
• US Class Current: 702/20
• 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 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

In one embodiment of the invention, an integrated system is used to analyze gene expression data. The system integrates

Claims

1. A method for analyzing gene expression comprising:

obtaining expression levels of a plurality of genes;

selecting at least one biological characteristic from a plurality of biological characteristics stored in a database;

wherein the biological characteristics comprise genomic information about the genes, structural information about the products of the genes; and

biological function of the genes; and

analyzing the expression levels according to the selected at least one biological characteristic.

2. The method of claim 1 wherein the analyzing comprises grouping the expression levels according to the selected at least one biological characteristic.

3. The method of claim 1 wherein the analyzing comprises selecting the expression levels for further analysis according to the selected at least one biological characteristic.

4. The method of claim 1 wherein the analyzing comprises clustering according to selected at least one biological characteristic.

5. The method of claim 4 wherein the analyzing comprises multiple dimensional clustering according to selected biological characteristics.

7. The method of claim 1 wherein the plurality of biological characteristics comprise orthologous genes.

8. The method of claim 1 wherein the plurality of biological characteristics comprise pathologic characteristics of genes.

9. The method of claim 1 wherein the plurality of biological characteristics comprise splice variant information.

10. The method of claim 1 wherein the plurality of biological characteristics comprise protein domain information.

11. The method of claim 1 wherein the plurality of biological characteristics comprise signal pathway information.

12. The method of claim 1 wherein the plurality of biological characteristics comprise gene ontology information.

13. The method of claim 1 wherein the database is a relational database.

14. The method of claim 1 wherein the database is an object oriented database.

15. The method of claim 13 wherein the biological characteristics are retrived using SQL statements.

17. The system of claim 16 wherein the analyzing comprises grouping the expression levels according to the selected at least one biological characteristic.

18. The system of claim 16 wherein the analyzing comprises selecting the expression levels for further analysis according to the selected at least one biological characteristic.

19. The system of claim 16 wherein the analyzing comprises clustering according to selected at least one biological characteristic.

20. The system of claim 16 wherein the analyzing comprises multiple dimensional clustering according to selected biological characteristics.

21. The system of claim 16 wherein the analyzing comprises data mining.

22. The system of claim 16 wherein the plurality of biological characteristics comprise orthologous genes.

23. The system of claim 16 wherein the plurality of biological characteristics comprise pathologic characteristics of genes.

24. The system of claim 16 wherein the plurality of biological characteristics comprise splice variant information.

25. The system of claim 16 wherein the plurality of biological characteristics comprise protein domain information.

26. The system of claim 16 wherein the plurality of biological characteristics comprise signal pathway information.

27. The system of claim 16 wherein the plurality of biological characteristics comprise gene ontology information.

28. The system of claim 16 wherein the database is a relational database.

29. The system of claim 16 wherein the database is an object oriented database.

30. The system of claim 28 wherein the biological characteristics are retrived using SQL statements.

6. The method of claim 6 wherein the analyzing comprises data mining.

16. A system for analyzing gene expression comprising a processor;

and a memory being coupled with the processor, the memory storing a plurality of machine instructions that cause the processor to perform the method steps of obtaining expression levels of a plurality of genes;

selecting at least one biological characteristic from a plurality of biological characteristics stored in a database;

wherein the biological characteristics comprise genomic information about the genes, structural information about the products of the genes; and

biological function of the genes; and

analyzing the expression levels according to the selected at least one biological characteristic.

31. A computer readable medium comprising computer-executable instructions for performing the methods comprising:

obtaining expression levels of a plurality of genes;

selecting at least one biological characteristic from a plurality of biological characteristics stored in a database;

wherein the biological characteristics comprise genomic information about the genes, structural information about the products of the genes; and

biological function of the genes; and

analyzing the expression levels according to the selected at least one biological characteristic.

32. The computer readable medium of claim 31 wherein the analyzing comprises grouping the expression levels according to the selected at least one biological characteristic.

33. The computer readable medium of claim 31 wherein the analyzing comprises selecting the expression levels for further analysis according to the selected at least one biological characteristic.

34. The computer readable medium of claim 31 wherein the analyzing comprises clustering according to selected at least one biological characteristic.

35. The computer readable medium of claim 31 wherein the analyzing comprises multiple dimensional clustering according to selected biological characteristics.

36. The computer readable medium of claim 31 wherein the analyzing comprises data mining.

37. The computer readable medium of claim 31 wherein the plurality of biological characteristics comprise orthologous genes.

38. The computer readable medium of claim 31 wherein the plurality of biological characteristics comprise pathologic characteristics of genes.

39. The computer readable medium of claim 31 wherein the plurality of biological characteristics comprise splice variant information.

40. The computer readable medium of claim 31 wherein the plurality of biological characteristics comprise protein domain information.

41. The computer readable medium of claim 31 wherein the plurality of biological characteristics comprise signal pathway information.

42. The computer readable medium of claim 31 wherein the plurality of biological characteristics comprise gene ontology information.

43. The computer readable medium of claim 31 wherein the database is a relational database.

44. The computer readable medium of claim 31 wherein the database is an object oriented database.

45. The computer readable medium of claim 43 wherein the biological characteristics are retrived using SQL statements.