System and method for retrieving and using gene expression data from multiple sources

• US 20030009295A1
• Filed: 03/14/2002
• Published: 01/09/2003
• Est. Priority Date: 03/14/2001
• Status: Abandoned Application

• Current Assignee: Gene Logic, Inc. (Steel Partners Holdings LP)
• Original Assignee: Gene Logic, Inc. (Steel Partners Holdings LP)
• Inventors: Chen, I-Min Amy, Markowitz, Victor, Topaloglou, Thodoros
• Application Number:
  US10/096,645
• Publication Number:
  US 20030009295A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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

Abstract

A method of analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, the method comprising: providing a data warehouse which comprises a gene expression database for storing quantitative gene expression measurements for tissues and cell lines screened using various assays; a clinical database for storing information on bio-samples and donors; and a fragment index for biological properties for DNA fragments; providing a connector which permits loading of more than one source of gene expression, gene annotation, and sample information, receiving a query regarding gene expression of one or more DNA fragments; determining the level of gene expression of the one or more DNA fragments; correlating the level of gene expression with the clinical database and the fragment index; and displaying the results of said correlation is disclosed.

Claims

1. A method of analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, the method comprising:

providing a data warehouse which comprises a gene expression database for storing quantitative gene expression measurements for tissues and cell lines screened using various assays;

a clinical database for storing information on bio-samples and donors; and

a fragment index for biological properties for DNA fragments;

providing a connector which permits loading of more than one source of gene expression, gene annotation, and sample information, receiving a query regarding gene expression of one or more DNA fragments;

determining the level of gene expression of the one or more DNA fragments;

correlating the level of gene expression with the clinical database and the fragment index; and

displaying the results of said correlation.

2. The method of claim 1, wherein the connector permits registering of more than one source of gene expression, gene annotation, and sample information and extraction of a list of experiments from the more than one source of gene expression, gene annotation, and sample information.

3. The method of claim 2, wherein the connector permits the refreshing of the list of experiments from the more than one source of gene expression, gene annotation, and sample information.

4. The method of claim 3, wherein the connector permits extraction and checking of a list of selected experiments from the more than one source of gene expression, gene annotation, and sample information.

5. The method of claim 4, wherein the method further comprises providing a staging database and wherein the connector permits migration of the more than one source of gene expression, gene annotation, and sample information from the staging database into the data warehouse.

6. The method of claim 5, wherein the connector permits loading of the more than one source of gene expression, gene annotation, and sample information into an analysis engine.

7. The method of claim 6, wherein the connector permits loading of the more than one source of gene expression, gene annotation, and sample information from XML files.

8. The method of claim 7, wherein the connector permits checking for consistency the more than one source of gene expression, gene annotation, and sample information.

9. The method of claim 8, wherein the method further comprises

providing a sample data editor and

wherein the connector permits updating of sample data with the sample data editor.

10. The method of claim 9, wherein the connector permits the providing of association between experiments and samples.

11. The method of claim 10, wherein the connector permits acquisition of such association from an XML sample file.

12. The method of claim 10, wherein the method further comprises

providing an expression data migration tool and

wherein the connector permits acquisition of such association from the an expression data migration tool.

14. The computer system of claim 13, wherein the connector permits registering of more than one source of gene expression, gene annotation, and sample information and extraction of a list of experiments from the more than one source of gene expression, gene annotation, and sample information.

15. The computer system of claim 14, wherein the connector permits the refreshing of the list of experiments from the more than one source of gene expression, gene annotation, and sample information.

16. The computer system of claim 15, wherein the connector permits extraction and checking of a list of selected experiments from the more than one source of gene expression, gene annotation, and sample information.

17. The computer system of claim 16, wherein the computer system further comprises

a staging database and

wherein the connector permits migration of the more than one source of gene expression, gene annotation, and sample information from the staging database into the data warehouse.

18. The computer system of claim 17, wherein the connector permits loading of the more than one source of gene expression, gene annotation, and sample information into an analysis engine.

19. The computer system of claim 18, wherein the connector permits loading of the more than one source of gene expression, gene annotation, and sample information from XML files.

20. The computer system of claim 19, wherein the connector permits checking for consistency the more than one source of gene expression, gene annotation, and sample information.

21. The computer system of claim 20, wherein the computer system further comprises

a sample data editor and

wherein the connector permits updating of sample data with the sample data editor.

22. The computer system of claim 21, wherein the connector permits the providing of association between experiments and samples.

23. The computer system of claim 22, wherein the connector permits acquisition of such association from an XML sample file.

24. The computer system of claim 22, wherein the computer system further comprises

an expression data migration tool and

wherein the connector permits acquisition of such association from the an expression data migration tool.

13. A computer system comprising

a data warehouse which comprises a gene expression database for storing quantitative gene expression measurements for tissues and cell lines screened using various assays;

a clinical database for storing information on bio-samples and donors; and

a fragment index for biological properties for DNA fragments;

a user interface capable of receiving a query regarding gene expression of one or more DNA fragments and displaying the results of a correlation of the level of gene expression with the clinical database and the fragment index; and

a connector which permits loading of more than one source of gene expression, gene annotation, and sample information.