METHOD AND APPARATUS FOR ANALYZING GENE INFORMATION FOR TREATMENT SELECTION

• US 20140019061A1
• Filed: 05/16/2013
• Published: 01/16/2014
• Est. Priority Date: 07/13/2012
• Status: Abandoned Application

• Current Assignee: Samsung Electronics Co. Ltd.
• Original Assignee: Samsung Electronics Co. Ltd.
• Inventors: AHN, Tae-jin, HONG, Seok-jin, SON, Dae-soon, BOPARDIKAR, Shyamsunder Ajit, MUKHERJEE, Subhankar, MALLAVARAPU, Rama Srikanth, LEE, Chon-hee
• Application Number:
  US13/896,079
• Publication Number:
  US 20140019061A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks

Abstract

A method and apparatus for analyzing information about a gene network in which genes included in a genome of an individual are classified into a plurality of subgroups based on functional correlations between the genes is acquired, and subgroups corresponding to an action of at least one drug to be used are visualized.

Claims

1. A method of analyzing gene information for treatment selection, the method comprising:

acquiring information about a gene network in which genes are classified into a plurality of subgroups based on functional correlations between the genes;

extracting gene subgroups that include a gene targeted by at least one drug to be used in treatment from among the plurality of subgroups included in the gene network; and

generating at least one index based on gene information included in the extracted subgroups to visualize the extracted subgroups,

wherein one or more of the steps of the method are performed using a gene analyzing apparatus.

2. The method of claim 1, wherein the at least one generated index includes an index for evaluating a genetic alteration level of each of the extracted subgroups, evaluating correlations between the extracted subgroups, or evaluating the number of genes included in the extracted subgroups.

3. The method of claim 1, wherein the generating of the at least one index comprises calculating a genetic alteration level of each of the extracted subgroups based on alteration levels of genes included in the extracted subgroups.

4. The method of claim 3, wherein the genetic alteration level of each of the extracted subgroups is calculated based on a statistical probability of which genes having a genetic alteration from among the genes included in a genome are included in each of the extracted subgroups.

5. The method of claim 3, wherein the genetic alteration level of each of the extracted subgroups is calculated using Geneset Analysis, Geneset Enrichment Analysis, Fisher Exact Test or combination thereof.

6. The method of claim 3, wherein the at least one generated index includes an index indicating each of the extracted subgroups with a different color according to a genetic alteration level of each of the extracted subgroups.

7. The method of claim 1, wherein the generating of the at least one index comprises calculating an index reflecting functional relatedness between genes included in the extracted subgroups.

8. The method of claim 7, wherein the functional relatedness is calculated using the number of genes functionally connected to each other between the extracted subgroups.

9. The method of claim 7, wherein the functional relatedness is calculated based on a result obtained by comparing the number of genes functionally connected to each other between the extracted subgroups with the number of genes functionally connected to each other between subgroups randomly sampled from the gene network.

10. The method of claim 1, wherein the generating of the at least one index comprises calculating an index reflecting the number of genes included in the extracted subgroups.

11. The method of claim 10, wherein the at least one generated index is an index indicating each of the extracted subgroups with a different size according to the number of genes included in the extracted subgroups.

12. The method of claim 1, further comprising generating a graphic representation of the at least one index applied to the extracted subgroups.

13. The method of claim 12, wherein the wherein the graphic representation shows the genes of the extracted subgroups as nodes connected to each other.

14. The method of claim 12, wherein the graphic representation shows extracted subgroups to which the at least one generated index is applied and the gene network, and wherein the graphic representation is displayed on a screen.

15. A non-transitory computer-readable recording medium storing a computer-readable program for executing the method of claim 1.

16. An apparatus for analyzing gene information for treatment selection, the apparatus comprising:

a data acquisition unit for acquiring information about a gene network in which genes are classified into a plurality of subgroups based on functional correlations between the genes;

a subgroup extracting unit for extracting gene subgroups that include a gene targeted by at least one drug to be used in treatment from among the plurality of subgroups included in the gene network; and

an index generating unit for generating at least one index based on gene information included in the extracted subgroups to visualize the extracted subgroups.

17. The apparatus of claim 16, wherein the at least one generated index includes an index for evaluating a genetic alteration level of each of the extracted subgroups, evaluating correlations between the extracted subgroups, or evaluating the number of genes included in the extracted subgroups.

18. The apparatus of claim 16, wherein the index generating unit calculates a genetic alteration level of each of the extracted subgroups based on alteration levels of genes included in the extracted subgroups.

19. The apparatus of claim 18, wherein the genetic alteration level of each of the extracted subgroups is calculated based on a statistical probability of which genes having a genetic alteration from among the genes included in a genome are included in each of the extracted subgroups.

20. The apparatus of claim 18, wherein the at least one generated index includes an index indicating each of the extracted subgroups with a different color according to a genetic alteration level of each of the extracted subgroups.

21. The apparatus of claim 16, wherein the index generating unit calculates an index reflecting functional relatedness between genes included in the extracted subgroups.

22. The apparatus of claim 21, wherein the functional relatedness is calculated using the number of genes functionally connected to each other between the extracted subgroups.

23. The apparatus of claim 16, wherein the index generating unit calculates an index reflecting the number of genes included in the extracted subgroups.

24. The apparatus of claim 23, wherein the at least one generated index is an index indicating each of the extracted subgroups with a different size according to the number of genes included in the extracted subgroups.

25. The apparatus of claim 16, further comprising a visualization processor for generating a graphic representation of the at least one index applied to the extracted subgroups.