Gene discovery for the system assignment of gene function

• US 7,623,969 B2
• Filed: 01/31/2002
• Issued: 11/24/2009
• Est. Priority Date: 01/31/2002
• Status: Active Grant

• Current Assignee: Institute for System Biology
• Original Assignee: Institute for System Biology
• Inventors: Ideker, Trey E., Hood, Leroy E., Siegel, Andrew F.
• Primary Examiner(s): Smith; Carolyn L.
• Application Number:
  US10/062,299
• Publication Number:
  US 20030143520A1
• Time in Patent Office: 2,854 Days
• Field of Search: 702/19, 435/6, 706/48
• US Class Current: 702/19
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface

Abstract

The invention provides a method for assigning a cellular function to a component of a biochemical system. The method involves (a) determining a multidimensional shape space for one or more components of a biochemical system in a reference state; (b) perturbing a component within said biochemical system; (c) determining a perturbed multidimensional shape space for one or more components of a pathway in said perturbed biochemical system, and (d) identifying a multidimensional coordinate point corresponding to a component of said perturbed pathway altered between reference and perturbed multidimensional shape spaces, said identified component being assigned a cellular function of said perturbed pathway.

Claims

1. A method for assigning a cellular function to a component of a biochemical system, comprising:

(a) physically perturbing a component of a network in a biochemical system;

(b) measuring a data element for each of n components of said perturbed biochemical system, wherein n is three or more;

(c) determining a multidimensional coordinate point in n-dimensional space representative of said data elements for each of said three or more measured components of said perturbed biochemical system, said multidimensional coordinate point comprising values for said data elements for each of said n measured components, wherein n corresponds to the number of measured biochemical components within said perturbed biochemical system;

(d) comparing said multidimensional coordinate point to a reference data element region;

(e) determining if said multidimensional coordinate point is within or outside said reference data element region, and

(f) providing an output to a user of said determination in step (e), wherein a multidimensional coordinate point outside of said reference data element region indicates that said component is linked to said perturbed biochemical network, and is thereby assigned a cellular function of said network.

2. The method of claim 1, wherein said data element is a data element selected from the group consisting of nucleic acid expression element and polypeptide expression element.

3. A method for assigning a cellular function to a component of a biochemical system, comprising:

(a) measuring a data element for each of n components of a physically perturbed biochemical system, wherein n is three or more;

(b) determining a multidimensional coordinate point in n-dimensional space representative of data elements for each of said three or more measured components in a biochemical network of said physically perturbed biochemical system, said multidimensional coordinate point comprising values for said data elements for each of said n measured components, wherein n corresponds to the number of measured biochemical components within said perturbed biochemical system;

(c) comparing said multidimensional coordinate point to a network-associated reference expression region of said set of components;

(d) determining if said multidimensional coordinate point is outside of said network-associated reference expression region, and

(e) providing an output to a user of said determination in step (d), wherein a multidimensional coordinate point outside of said network-associated reference expression region indicates a perturbed state of said network, said component being linked to said perturbed network and thereby being assigned a cellular function of said network.

4. The method of claim 3, wherein said biochemical system is selected from the group consisting of a cell, tissue, organism and subcellular system.

5. The method of claim 3, wherein said data element is an expression data element.

6. The method of claim 3, wherein said reference expression region indicates a normal state of a biochemical system.

7. The method of claim 3, wherein said components of the biochemical network comprise nucleic acids.

8. The method of claim 3, wherein said components of the biochemical network comprise polypeptides.

9. A method for assigning a cellular function to a component of a biochemical system, comprising:

(a) measuring a data element for each of n components of a physically perturbed biochemical system, wherein n is three or more;

(b) determining a multidimensional coordinate point in n-dimensional space representative of data elements of said three or more measured components in a biochemical pathway of said physically perturbed biochemical system, said multidimensional coordinate point comprising values for said data elements for each of said n measured components, wherein n corresponds to the number of measured biochemical components within said perturbed biochemical system;

(c) comparing said multidimensional coordinate point to a pathway-associated reference expression region of said set of components;

(d) determining if said multidimensional coordinate point is outside of said pathway-associated reference expression region, and

(e) providing an output to a user of said determination in step (d), wherein a multidimensional coordinate point outside of said pathway-associated reference expression region indicates a perturbed state of said pathway, said component being linked to said perturbed pathway and thereby being assigned a cellular function of said pathway.

10. The method of claim 9, wherein said biochemical system is selected from the group consisting of a cell, tissue, organism and subcellular system.

11. The method of claim 9, wherein said data element is an expression data element.

12. The method of claim 9, wherein said reference expression region indicates a normal state of a biochemical system.

13. The method of claim 9, wherein said components of the biochemical network comprise nucleic acids.

14. The method of claim 9, wherein said components of the biochemical network comprise polypeptides.