METHODS AND GENE EXPRESSION SIGNATURE FOR ASSESSING GROWTH FACTOR SIGNALING PATHWAY REGULATION STATUS

• US 20110015869A1
• Filed: 03/19/2009
• Published: 01/20/2011
• Est. Priority Date: 03/22/2008
• Status: Active Grant

• Current Assignee: Merck Sharp & Dohme Corporation (Merck & Co., Inc.)
• Original Assignee: Merck Sharp & Dohme Corporation (Merck & Co., Inc.)
• Inventors: Nebozhyn, Michael, Watters, James, Loboda, Andrey
• Granted Patent: US 8,392,127 B2
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/158 Expression markers
• 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 40/20 Supervised data analysis

Abstract

Methods, biomarkers, and expression signatures are disclosed for assessing the regulation status of growth factor pathway signaling in a cell sample or subject. More specifically, several aspects of the invention provide a set of genes which can be used as biomarkers and gene signatures for evaluating growth factor pathway deregulation status in a sample; classifying a cell sample as having a deregulated or regulated growth factor signaling pathway; determining whether an agent modulates the growth factor signaling pathway in sample; predicting response of a subject to an agent that modulates the growth factor signaling pathway; assigning treatment to a subject; and predicting evaluating the pharmacodynamic effects of cancer therapies designed to regulate growth factor pathway signaling.

Claims

1. A method for classifying an isolated cell sample as having a deregulated or regulated growth factor signaling pathway, comprising:

(i) calculating a measure of similarity between a first expression profile and a regulated growth factor signaling pathway template, said first expression profile comprising the expression levels of a first plurality of genes in the tumor cell sample, said regulated growth factor signaling pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell samples not having at least one or more components of said growth factor signaling pathway with abnormal activity, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Tables 5a and 5b;

(ii) classifying said tumor cell sample as having said regulated growth factor signaling pathway if said first expression profile has a high similarity to said regulated growth factor signaling pathway template, or classifying said tumor cell sample as having said deregulated growth factor signaling pathway if said first expression profile has a low similarity to said regulated growth factor signaling pathway template;

wherein said first expression profile has a high similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is above a predetermined threshold, or has a low similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

8. The method of claim 1 or 2, wherein the isolated cell sample is from a human subject.

9. The method of claim 1, wherein said first plurality consists of at least 10 of the genes for which biomarkers are listed in Tables 5a and 5b.

10. The method of claim 1, wherein said first plurality consists of at least 20 of the genes for which biomarkers are listed in Tables 5a and 5b.

11. The method of claim 1, wherein said first plurality consists of at least 50 of the genes for which biomarkers are listed in Tables 5a and 5b.

46. The method of claim 1, wherein said first plurality consists of at least 20 of the genes for which biomarkers are listed in Tables 11a and 11b.

2. A method for classifying an isolated cell sample as having a deregulated or regulated growth factor signaling pathway, comprising

(i) calculating a signature score by a method comprising:

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in the cell sample relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said cell sample as having a deregulated growth factor signaling pathway a) if said obtained signature score is above a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

3. The method of claim 2, wherein said first plurality of genes consists of at least 3 or more of the genes for which biomarkers are listed in Table 9a and said second plurality of genes consists of at least 3 or more genes for which biomarkers are listed in Table 9b.

4. The method of claim 2, wherein said differential expression value is log(10) ratio.

5. The method of claim 2, wherein said differential expression value is log 10(2̂

-Ct).

6. The method of claim 2, wherein said threshold is 0.

7. The method of claim 2, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

12. The method of claim 2, wherein said first plurality consists of at least 5 of the genes for which biomarkers are listed in Table 5a and said second plurality consists of at least 5 of the genes for which biomarkers are listed in Table 5b.

15. The method of claim 12, wherein said first plurality of genes consists of at least 3 or more of the genes for which biomarkers are listed in Table 9a and said second plurality of genes consists of at least 3 or more genes for which biomarkers are listed in Table 9b.

16. The method of claim 12, wherein said differential expression value is log(10) ratio.

17. The method of claim 12, wherein said differential expression value is log 10(2̂

-Ct).

18. The method of claim 12, wherein said threshold is 0.

19. The method of claim 12, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

13. A method for predicting response of a subject to an agent that modulates the growth factor signaling pathway, said method comprising:

(a) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a measure of similarity between a first expression profile and a regulated growth factor signaling pathway template, said first expression profile comprising the expression levels of a first plurality of genes in an isolated cell sample derived from said subject, said regulated growth factor signaling pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell sample not having at least one or more components of said growth factor signaling pathway with abnormal activity, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Tables 5a and 5b;

(ii) classifying said cell sample as having said regulated growth factor signaling pathway if said first expression profile has a high similarity to said regulated growth factor signaling pathway template, or classifying said cell sample as having said deregulated growth factor signaling pathway if said first expression profile has a low similarity to said regulated growth factor signaling pathway template;

wherein said first expression profile has a high similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is above a predetermined threshold, or has a low similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

wherein a subject classified as having deregulated growth factor signaling pathway is indicative of a subject that is predicted to respond to the agent.

14. A method for predicting response of a subject to an agent that modulates the growth factor signaling pathway, said method comprising:

(a) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a deregulated growth factor signaling pathway a) if said obtained signature score is above a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject classified as having deregulated growth factor signaling pathway is indicative of a subject that is predicted to respond to the agent.

20. A method of assigning treatment to a subject, said method comprising:

(a) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a deregulated growth factor signaling pathway a) if said obtained signature score is above a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

(b) assigning said subject with an agent that modulates said growth factor signaling pathway, and not assigning said cancer patient with a mitotic inhibitor type agent, if said subject is classified as having deregulated growth factor signaling pathway.

21. The method of claim 20, wherein said first plurality of genes consists of at least 3 or more of the genes for which biomarkers are listed in Table 9a and said second plurality of genes consists of at least 3 or more genes for which biomarkers are listed in Table 9b.

22. The method of claim 20, wherein said differential expression value is log(10) ratio.

23. The method of claim 20, wherein said differential expression value is log 10(2̂

-Ct).

24. The method of claim 20, wherein said threshold is 0.

25. The method of claim 20, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

26. A method of measuring pharmacodynamic activity of an agent on the growth factor signaling pathway in a subject, comprising:

(a) contacting a subject with an agent that modulates one or more components of growth factor signaling pathway;

(b) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a regulated growth factor signaling pathway a) if said obtained signature score is below a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject treated with said agent and classified as having regulated growth factor signaling pathway is indicative of an agent with pharmacodynamic activity on the growth factor signaling pathway.

27. The method of claim 26, wherein said first plurality of genes consists of at least 3 or more of the genes for which biomarkers are listed in Table 9a and said second plurality of genes consists of at least 3 or more genes for which biomarkers are listed in Table 9b.

28. The method of claim 26, wherein said differential expression value is log(10) ratio.

29. The method of claim 26, wherein said differential expression value is log 10(2̂

-Ct).

30. The method of claim 26, wherein said threshold is 0.

31. The method of claim 26, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

32. A method of determining whether an agent modulates the growth factor signaling pathway in a subject, comprising:

(a) contacting a subject with an agent;

(b) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample not contacted with said agent, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 5b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a regulated growth factor signaling pathway a) if said obtained signature score is below a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject treated with said agent and classified as having regulated growth factor signaling pathway is indicative of an agent with an effect on the growth factor signaling pathway.

33. The method of claim 32, wherein said first plurality of genes consists of at least 3 or more of the genes for which biomarkers are listed in Table 9a and said second plurality of genes consists of at least 3 or more genes for which biomarkers are listed in Table 9b.

34. The method of claim 32, wherein said differential expression value is log(10) ratio.

35. The method of claim 32, wherein said differential expression value is log 10(2̂

-Ct).

36. The method of claim 32, wherein said threshold is 0.

37. The method of claim 32, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

38. A method for classifying an isolated cell sample as having a deregulated or regulated growth factor signaling pathway, comprising:

(i) calculating a measure of similarity between a first expression profile and a regulated growth factor signaling pathway template, said first expression profile comprising the expression levels of a first plurality of genes in the tumor cell sample, said regulated growth factor signaling pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell samples not having at least one or more components of said growth factor signaling pathway with abnormal activity, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Tables 11a and 11b;

(ii) classifying said tumor cell sample as having said regulated growth factor signaling pathway if said first expression profile has a high similarity to said regulated growth factor signaling pathway template, or classifying said tumor cell sample as having said deregulated growth factor signaling pathway if said first expression profile has a low similarity to said regulated growth factor signaling pathway template;

wherein said first expression profile has a high similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is above a predetermined threshold, or has a low similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

44. The method of claim 38 or 39, wherein the isolated cell sample is from a human subject.

45. The method of claim 38, wherein said first plurality consists of at least 10 of the genes for which biomarkers are listed in Tables 11a and 11b.

47. The method of claim 38, wherein said first plurality consists of at least 50 of the genes for which biomarkers are listed in Tables 11a and 11b.

39. A method for classifying an isolated cell sample as having a deregulated or regulated growth factor signaling pathway, comprising

(i) calculating a signature score by a method comprising:

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in the cell sample relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said cell sample as having a deregulated growth factor signaling pathway a) if said obtained signature score is above a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

40. The method of claim 39, wherein said differential expression value is log(10) ratio.

41. The method of claim 39, wherein said differential expression value is log 10(2̂

-Ct).

42. The method of claim 39, wherein said threshold is 0.

43. The method of claim 39, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

48. The method of claim 39, wherein said first plurality consists of at least 5 of the genes for which biomarkers are listed in Table 11a and said second plurality consists of at least 5 of the genes for which biomarkers are listed in Table 11b.

49. A method for predicting response of a subject to an agent that modulates the growth factor signaling pathway, said method comprising:

(a) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a measure of similarity between a first expression profile and a regulated growth factor signaling pathway template, said first expression profile comprising the expression levels of a first plurality of genes in an isolated cell sample derived from said subject, said regulated growth factor signaling pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell sample not having at least one or more components of said growth factor signaling pathway with abnormal activity, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Tables 11a and 11b;

(ii) classifying said cell sample as having said regulated growth factor signaling pathway if said first expression profile has a high similarity to said regulated growth factor signaling pathway template, or classifying said cell sample as having said deregulated growth factor signaling pathway if said first expression profile has a low similarity to said regulated growth factor signaling pathway template;

wherein said first expression profile has a high similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is above a predetermined threshold, or has a low similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

wherein a subject classified as having deregulated growth factor signaling pathway is indicative of a subject that is predicted to respond to the agent.

50. A method for predicting response of a subject to an agent that modulates the growth factor signaling pathway, said method comprising:

(a) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential, expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a deregulated growth factor signaling pathway a) if said obtained signature score is above a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject classified as having deregulated growth factor signaling pathway is indicative of a subject that is predicted to respond to the agent.

51. The method of claim 50, wherein said differential expression value is log(10) ratio.

52. The method of claim 50, wherein said differential expression value is log 10(2̂

-Ct).

53. The method of claim 50, wherein said threshold is 0.

54. The method of claim 50, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

55. A method of assigning treatment to a subject, said method comprising:

(a) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a deregulated growth factor signaling pathway a) if said obtained signature score is above a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

(b) assigning said subject with an agent that modulates said growth factor signaling pathway, and not assigning said cancer patient with a mitotic inhibitor type agent, if said subject is classified as having deregulated growth factor signaling pathway.

56. The method of claim 55, wherein said differential expression value is log(10) ratio.

57. The method of claim 55, wherein said differential expression value is log 10(2̂

-Ct).

58. The method of claim 55, wherein said threshold is 0.

59. The method of claim 55, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

60. A method of measuring pharmacodynamic activity of an agent on the growth factor signaling pathway in a subject, comprising:

(a) contacting a subject with an agent that modulates one or more components of growth factor signaling pathway;

(b) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a regulated growth factor signaling pathway a) if said obtained signature score is below a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject treated with said agent and classified as having regulated growth factor signaling pathway is indicative of an agent with pharmacodynamic activity on the growth factor signaling pathway.

61. The method of claim 60, wherein said differential expression value is log(10) ratio.

62. The method of claim 60, wherein said differential expression value is log 10(2̂

-Ct).

63. The method of claim 60, wherein said threshold is 0.

64. The method of claim 60, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

65. A method of determining whether an agent modulates the growth factor signaling pathway in a subject, comprising:

(a) contacting a subject with an agent;

(b) classifying said subject as having a deregulated or regulated growth factor signaling pathway, wherein said classifying comprises;

(i) calculating a signature score by a method comprising;

a) calculating a differential expression value of a first expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated cell sample derived from said subject relative to a second expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample not contacted with said agent, said first plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11a and said second plurality of genes consisting of at least 3 or more of the genes for which biomarkers are listed in Table 11b;

b) calculating the mean differential expression values of the expression levels of said first plurality of genes and said second plurality of genes; and

c) subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes to obtain said signature score;

(ii) classifying said subject as having a regulated growth factor signaling pathway a) if said obtained signature score is below a predetermined threshold, and b) if said signature score is statistically significant; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject treated with said agent and classified as having regulated growth factor signaling pathway is indicative of an agent with an effect on the growth factor signaling pathway.

66. The method of claim 65, wherein said differential expression value is log(10) ratio.

67. The method of claim 65, wherein said differential expression value is log 10(2̂

-Ct).

68. The method of claim 65, wherein said threshold is 0.

69. The method of claim 65, wherein said signature scores is statistically significant if it has a p-value less than 0.05.

70. A method for classifying an isolated cell sample as having an activated or non-activated glycolysis pathway, comprising:

(i) calculating a measure of similarity between a first expression profile and non-activated glycolysis pathway template, said first expression profile comprising the expression levels of a first plurality of genes in the tumor cell sample, said non-activated glycolysis pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell samples not having significant glycolysis activity in the presence of oxygen, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Table 13;

(ii) classifying said tumor cell sample as having said non-activated glycolysis pathway if said first expression profile has a high similarity to said non-activated glycolysis pathway template, or classifying said tumor cell sample as having said activated glycolysis pathway if said first expression profile has a low similarity to said non-activated glycolysis pathway template;

wherein said first expression profile has a high similarity to non-activated glycolysis pathway template if the similarity to said non-activated glycolysis pathway template is above a predetermined threshold, or has a low similarity to said non-activated glycolysis pathway template if the similarity to said non-activated glycolysis pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

71. The method of claim 70, wherein the isolated cell sample is from a human subject.

72. The method of claim 70, wherein said first plurality consists of at least 10 of the genes for which biomarkers are listed in Table 13.

73. The method of claim 70, wherein said first plurality consists of at least 20 of the genes for which biomarkers are listed in Tables 13.

74. A method for predicting response of a subject to an agent that modulates the glycolysis pathway, said method comprising:

(a) classifying said subject as having an activated or non-activated glycolysis pathway, wherein said classifying comprises;

(i) calculating a measure of similarity between a first expression profile and a non-activated glycolysis pathway template, said first expression profile comprising the expression levels of a first plurality of genes in an isolated cell sample derived from said subject, said non-activated glycolysis pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell sample not having significant glycolysis activity in the presence of oxygen, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Table 13;

(ii) classifying said cell sample as having said non-activated glycolysis pathway if said first expression profile has a high similarity to said non-activated glycolysis pathway template, or classifying said cell sample as having said activated glycolysis pathway if said first expression profile has a low similarity to said non-activated glycolysis pathway template;

wherein said first expression profile has a high similarity to said non-activated glycolysis pathway template if the similarity to said non-activated glycolysis pathway template is above a predetermined threshold, or has a low similarity to said non-activated glycolysis pathway template if the similarity to said non-activated glycolysis pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii).

wherein a subject classified as having activated glycolysis pathway is indicative of a subject that is predicted to respond to the agent.

75. The method of claim 74, wherein the isolated cell sample is from a human subject.

76. The method of claim 74, wherein said first plurality consists of at least 10 of the genes for which biomarkers are listed in Table 13.

77. The method of claim 74, wherein said first plurality consists of at least 20 of the genes for which biomarkers are listed in Tables 13.

78. A method of determining whether an agent modulates the glycolysis pathway in a subject, comprising:

(a) contacting a subject with an agent;

(b) classifying said subject as having a non-activated or activated glycolysis pathway, wherein said classifying comprises;

(i) calculating a measure of similarity between a first expression profile and a non-activated glycolysis pathway template, said first expression profile comprising the expression levels of a first plurality of genes in an isolated cell sample derived from said subject, said non-activated glycolysis pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell sample not having significant glycolysis activity in the presence of oxygen, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Table 13;

(ii) classifying said cell sample as having said non-activated glycolysis pathway if said first expression profile has a high similarity to said non-activated glycolysis pathway template, or classifying said cell sample as having said activated glycolysis pathway if said first expression profile has a low similarity to said non-activated glycolysis pathway template;

wherein said first expression profile has a high similarity to said non-activated glycolysis pathway template if the similarity to said non-activated glycolysis pathway template is above a predetermined threshold, or has a low similarity to said non-activated glycolysis pathway template if the similarity to said non-activated glycolysis pathway template is below said predetermined threshold; and

(iii) displaying;

or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system;

the classification produced by said classifying step (ii);

wherein a subject treated with said agent and classified as having non-activated glycolysis pathway is indicative of an agent with an effect on the glycolysis pathway.

79. The method of claim 78, wherein the isolated cell sample is from a human subject.

80. The method of claim 78, wherein said first plurality consists of at least 10 of the genes for which biomarkers are listed in Table 13.

81. The method of claim 78, wherein said first plurality consists of at least 20 of the genes for which biomarkers are listed in Tables 13.