System and method for managing gene expression data

• US 20030171876A1
• Filed: 03/05/2002
• Published: 09/11/2003
• Est. Priority Date: 03/05/2002
• Status: Abandoned Application

• Current Assignee: Gene Logic, Inc. (Steel Partners Holdings LP)
• Original Assignee: Gene Logic, Inc. (Steel Partners Holdings LP)
• Inventors: Campbell, John, Dolginow, Doug, McLoughlin, Kevin, Topaloglou, Thodoros, Kosky, Anthony, Krylov, Dmitry, Chen, I-Min A., Markowitz, Victor
• Application Number:
  US10/090,144
• Publication Number:
  US 20030171876A1
• 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 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

The present invention pertains to a system and method of analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, 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; 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.

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;

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 data warehouse is constructed in a star relational schema.

3. The method of claim 1, wherein the data warehouse is constructed in a snowflake relational schema.

4. The method of claim 1, wherein the analysis of gene expression, gene annotation, and sample information further comprises identifying two sets of DNA fragments:

those that are consistently expressed within the sample set, and those that are consistently not expressed.

5. The method of claim 1, wherein the analysis of gene expression, gene annotation, and sample information further comprises a gene signature differential analysis which compares two gene expression signature and derives four sets of DNA gene fragments:

those that are in both the first gene signature'"'"'s present gene set and the second'"'"'s absent gene set, those that are in both the first gene signature'"'"'s absent gene set and the second'"'"'s present gene set, those that are in both present gene sets, those that are in both absent gene sets.

6. The method of claim 1, wherein the analysis of gene expression, gene annotation, and sample information further comprises a fold change analysis which quantifies the change in expression for differentially expressed genes between pairs of DNA fragments.

7. The method of claim 1, wherein the analysis of gene expression, gene annotation, and sample information further comprises an E Northern analysis which identifies DNA fragments with regard to a pair of user-selected percentiles over the values for a sample.

8. 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 and

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.

9. The computer of claim 8, wherein the data warehouse is constructed in a star relational schema.

10. The computer of claim 8, wherein the data warehouse is constructed in a snowflake relational schema.

11. The computer of claim 8, wherein the analysis of gene expression, gene annotation, and sample information further comprises identifying two sets of DNA fragments:

those that are consistently expressed within the sample set, and those that are consistently not expressed.

12. The computer of claim 8, wherein the analysis of gene expression, gene annotation, and sample information further comprises a gene signature differential analysis which compares two gene expression signature and derives four sets of DNA gene fragments:

those that are in both the first gene signature'"'"'s present gene set and the second'"'"'s absent gene set,

those that are in both the first gene signature'"'"'s absent gene set and the second'"'"'s present gene set,

those that are in both present gene sets, those that are in both absent gene sets.

13. The computer of claim 8, wherein the analysis of gene expression, gene annotation, and sample information further comprises a fold change analysis which quantifies the change in expression for differentially expressed genes between pairs of DNA fragments.

14. The computer of claim 8, wherein the analysis of gene expression, gene annotation, and sample information further comprises an E Northern analysis which identifies DNA fragments with regard to a pair of user-selected percentiles over the values for a sample.

15. A computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to 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;

the computer program product comprising computer-readable program code for effecting the following steps within a computing system;

providing an interface for 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 S index; and

displaying the results of said correlation.

16. The computer program product of claim 15, wherein the data warehouse is constructed in a star relational schema.

17. The computer program product of claim 15, wherein the data warehouse is constructed in a snowflake relational schema.

18. The computer program product of claim 15, wherein the analysis of gene expression, gene annotation, and sample information further comprises identifying two sets of DNA fragments:

those that are consistently expressed within the sample set, and those that are consistently not expressed.

19. The method of claim 15, wherein the analysis of gene expression, gene annotation, and sample information further comprises a gene signature differential analysis which compares two gene expression signature and derives four sets of DNA gene fragments:

those that are in both the first gene signature'"'"'s present gene set and the second'"'"'s absent gene set,

those that are in both the first gene signature'"'"'s absent gene set and the second'"'"'s present gene set,

those that are in both present gene sets, those that are in both absent gene sets.

20. The computer program product of claim 15, wherein the analysis of gene expression, gene annotation, and sample information further comprises a fold change analysis which quantifies the change in expression for differentially expressed genes between pairs of DNA fragments.

21. The method of claim 15, wherein the analysis of gene expression, gene annotation, and sample information further comprises an E Northern analysis which identifies DNA fragments with regard to a pair of user-selected percentiles over the values for a sample.