Method and system for analyzing biological response signal data

• US 6,453,241 B1
• Filed: 12/23/1998
• Issued: 09/17/2002
• Est. Priority Date: 12/23/1998
• Status: Expired due to Fees

• Current Assignee: Microsoft Technology Licensing LLC (Microsoft Corporation)
• Original Assignee: Rosetta Inpharmatics Incorporated
• Inventors: Bondarenko, Andrey, Buskirk, Stewart, Bassett, Douglas Jr.
• Primary Examiner(s): Brusca, John S.
• Application Number:
  US09/220,276
• Time in Patent Office: 1,364 Days
• Field of Search: 702/19, 702/20, 702/21, 435/6, 706/15-23
• US Class Current: 702/19
• CPC Class Codes: G06F 2221/2145 Inheriting rights or properties, e.g., propagation of permissions or restrictions within a hierarchy
• 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 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration

Abstract

A system, method, and computer program product for enhanced computer-aided analysis of biological response data is disclosed. In a preferred embodiment, biological datasets are graphically selected by a user from a first active biological viewer window on a user computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in the destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. In another preferred embodiment, hierarchical cluster trees from biological signal profiles are presented in a hyperbolic display fashion. In another preferred embodiment, biological menu and submenu items utilized by the user computer are not stored in the user computer, but rather are stored a central biological response database. Biological menus and submenus are generated at startup time based on queries to the central biological response database, allowing for increased flexibility, changeability, and customization of the biological menus. In another preferred embodiment, correlation data between biological signal profile data is precomputed when the experiments are added to the central biological response database, eliminating the need for real time computation of correlation coefficients by the user computer.

Claims

1. A method for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user comprising the steps of:

storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

receiving a command from said user to initiate a comparison algorithm, said command identifying a query profile selected from among said plurality of biological signal profiles in said computer database;

computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user.

19. The method of claim 1, 2, 8, or 9 wherein said computer database is a relational database.

20. The method of claim 1, 2, 8 or 9 wherein said computer database is an object oriented database.

21. The method of claim 1, 2, 8, or 9 wherein said plurality of biological signal profiles comprise gene expression level data.

24. The method of claim 1, 2, 8, or 9 wherein said plurality of biological signal profiles comprise protein expression level data.

35. The method of claim 1 or 8, wherein each said similarity metric in said plurality of similarity metrics consists of a single scalar correlation coefficient.

36. The method of claim 1 or 8, wherein each said similarity metric in said plurality of similarity metrics consists of a multidimensional correlation matrix.

37. The method of claim 1 or 8, further comprising the step of storing said plurality of similarity metrics in said computer database.

38. The method of claim 1 or 8 further comprising a step of selecting the data points of said query profile and the corresponding data points of each said different target profile between which said plurality of similarity metrics is computed.

40. The method of claim 1, 2, 8 or 9, wherein said step of receiving said command comprises a step of selecting said query profile and each said different target profile.

57. The method of claim 40, said step of selecting said query profile and each said different target profile comprising the steps of displaying a search menu and receiving search menu and alphanumeric inputs from the user.

58. The method of claim 40, said step of selecting said query profile and each said different target profile comprising the step of receiving a graphical selection command from the user.

70. The method of claim 1 wherein at least one biological signal profile used in an instance of said computing step comprises data points measured in response to a perturbation to a cell or an organism.

2. A method for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user comprising the steps of:

storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

computing a plurality of similarity metrics, each similarity metric being computed in accordance with a comparison algorithm between (i) data points of a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

storing said plurality of similarity metrics in said computer database in computer readable form;

receiving a command from said user to initiate said comparison algorithm, said command identifying said query profile;

retrieving from said computer database said plurality of similarity metrics; and

communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user.

39. The method of claim 2 or 9 further comprising a step of selecting the data points of said query profile and the corresponding data points of each said different target profile between which said plurality of similarity metrics is computed.

59. The method of claim 2, wherein said step of receiving said command from said user to initiate said comparison algorithm is executed at a time subsequent to said step of computing said plurality of similarity metrics.

71. The method of claim 2 wherein at least one biological signal profile used in an instance of said computing step comprises data points measured in response to a perturbation to a cell or an organism.

3. A computer program product for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, said computer program product comprising on computer readable medium:

computer code for storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

computer code for receiving a command from said user to initiate a comparison algorithm, said command identifying a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

computer code for computing a plurality of similarity metrics, in accordance with said comparison algorithm, between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

computer code for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user.

72. The computer program product of claim 3 wherein at least one biological signal profile used by said computer code for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

4. A computer program product for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, said computer program product comprising on computer readable medium:

computer code for storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

computer code for computing a plurality of similarity metrics, each similarity metric being computed in accordance with a comparison algorithm between (i) data points of a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

computer code for storing said plurality of similarity metrics in said computer database in computer readable form;

computer code for receiving a command from said user to initiate said comparison algorithm, said command identifying said query profile;

computer code for retrieving from said computer database said plurality of similarity metrics; and

computer code for communicating as an ordered list said plurality of similarity metrics, or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user.

60. The computer program product of claim 4 wherein said computer code for receiving said command from said user to initiate said comparison algorithm is to be executed at a time subsequent to execution of said computer code for computing said plurality of similarity metrics.

73. The computer program product of claim 4 wherein at least one biological signal profile used by said computer code for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

5. A computer system for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, the computer system comprising:

one or more processors;

storage media for storing a computer database;

a program module, executable by said one or more processors, for processing said biological signal profile data, said program module comprising;

instructions for storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

instructions for receiving a command from said user to initiate a comparison algorithm, said command identifying a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

instructions for computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user.

74. The computer system of claim 5 wherein at least one biological signal profile used by said instructions for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

6. A computer system for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, the computer system comprising:

one or more processors;

storage media for storing a computer database;

a program module, executable by said one or more processors, for processing said biological signal profile data, said program module comprising;

instructions for storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

instructions for computing a plurality of similarity metrics, each similarity metric being computed in accordance with a comparison algorithm, between (i) data points of a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

instructions for receiving a command from said user to initiate said comparison algorithm, said command identifying said query profile;

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list begin ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user;

wherein said instructions for receiving said command from said user to initiate said comparison algorithm are to be executed at a time subsequent to execution of said instructions for computing said similarity metrics.

18. The computer system of claim 6, wherein said plurality of similarity metrics is to be computed by said instructions for computing said plurality of similarity metrics using said one or more processors at a time prior to execution of said instructions for receiving said command from said user to initiate said comparison algorithm, thereby decreasing a time required until said instructions for communicating are initiated.

75. The computer system of claim 6 wherein at least one biological signal profile used by said instructions for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

7. A computer system for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, said computer system comprising:

one or more processors;

storage media for storing a computer database;

a program module, executable by said one or more processors, for processing said biological signal profile data, said program module comprising;

instructions for storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

instructions for computing a plurality of similarity metrics, each similarity metric being computed in accordance with a comparison algorithm between (i) data points of a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

instructions for storing said plurality of similarity metrics in said computer database in computer readable form;

instructions for receiving a command from said user to initiate said comparison algorithm, said command identifying said query profile;

instructions for retrieving from said computer database said plurality of similarity metrics; and

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data for storage in said computer database and for retrieval therefrom by said user.

62. The computer system of claim 7 wherein said instructions for receiving said command from said user to initiate said comparison algorithm are to be executed at a time subsequent to execution of said instructions for computing said plurality of similarity metrics.

76. The computer system of claim 7 wherein at least one biological signal profile used by said instructions for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

8. A method for processing biological signal profile data comprising the steps of:

receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in computer readable form in a computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data.

77. The method of claim 8 wherein at least one biological signal profile used in an instance of said computing step comprises data points measured in response to a perturbation to a cell or an organism.

9. A method for processing biological signal profile data comprising the steps of:

receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in computer readable form in a computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

retrieving, from said computer database, a plurality of similarity metrics stored in computer readable form in said computer database, each similarity metric having been computed, in accordance with said comparison algorithm, between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data.

78. The method of claim 9 wherein at least one biological signal profile used in an instance of said computing step comprises data points measured in response to a perturbation to a cell or an organism.

10. A computer program product for processing biological signal profile data, said computer program product comprising on computer readable medium:

computer code for receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in computer readable form in a computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

computer code for computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

computer code for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data.

22. The computer program product of claim 3, 4, 10 or 11 wherein said plurality of biological signal profile comprise gene expression level data.

25. The computer program product of claim 3, 4, 10 or 11 wherein said plurality of biological signal profiles comprise protein expression level data.

41. The computer program product of claim 3 or 10, wherein each said similarity metric in said plurality of similarity metrics consists of a single scalar correlation coefficient.

42. The computer program product of claim 3 or 10, wherein each said similarity metric in said plurality of similarity metrics consists of a multidimensional correlation matrix.

43. The computer program product of claim 3 or 10, said computer program product further comprising computer code for storing said plurality of similarity metrics in said computer database.

44. The computer program product of claim 3 or 10, further comprising computer code for user directed selection of the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics is computed.

61. The computer program product of claim 3 or 10 wherein said computer code for receiving said command from said user to initiate said comparison algorithm is to be executed at a time subsequent to execution of said computer code for computing said plurality of similarity metrics.

79. The computer program product of claim 10 wherein at least one biological signal profile used by said computer code for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

11. A computer program product for processing biological signal profile data, said computer program product comprising on computer readable medium:

computer code for receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in computer readable form in a computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

computer code for retrieving, from said computer database, a plurality of similarity metrics stored in computer readable form in said computer database, each similarity metric in said plurality of similarity metrics having been computed in accordance with said comparison algorithm between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

computer code for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data.

45. The computer program product of claim 4 or 11, further comprising computer code for user directed selection of the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics is computed.

46. The computer program product of claim 45, wherein said computer code for receiving said command comprises computer code for selecting said query profile and each said different target profile.

47. The computer program product of claim 46, said computer code for selecting said query profile and each said different target profile comprising:

computer code for displaying a search menu; and

computer code for receiving search menu and alphanumeric inputs from the user.

48. The computer program product of claim 46, said computer code for selecting said query profile and each said different target profile comprising:

computer code for receiving a graphical selection command from the user.

80. The computer program product of claim 11 wherein at least one biological signal profile used by said computer code for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

12. A computer system for processing biological signal profile data, the computer system comprising:

one or more processors;

storage media for storing a computer database;

a program module, executable by said one or more processors, for processing said biological signal profile data, said program module comprising;

instructions for receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

instructions for computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data.

23. The computer system of claim 5, 7, 12 or 13, wherein said plurality of biological signal profiles comprise gene expression level data.

26. The computer system of claim 5, 7, 12 or 13, wherein said plurality of biological signal profiles comprise protein expression level data.

49. The computer system of claim 5 or 12, wherein each said similarity metric in said plurality of similarity metrics consists of a single scalar correlation coefficient.

50. The computer system of claim 5 or 12, wherein each said similarity metric in said plurality of similarity metrics consists of a multidimensional correlation matrix.

51. The computer system of claim 5 or 12, said program module further comprising instructions for storing said plurality of similarity metrics in said computer database.

52. The computer system of claim 5 or 12, wherein said program module further comprises instructions for user directed selection of the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics are computed.

54. The computer system of claim 5, 7, 12, or 13, wherein said instructions for receiving said command comprises instructions for selecting said query profile and each said different target profile.

55. The computer system of claim 54, said instructions for selecting said query profile and each said different target profile comprising:

instructions for displaying a search menu; and

instructions for receiving search menu and alphanumeric inputs from the user.

56. The computer system of claim 54, said instructions for selecting said query profile and each said different target profile comprising:

instructions for receiving a graphical selection command from the user.

81. The computer system of claim 12 wherein at least one biological signal profile used by said instructions for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

13. A computer system for processing biological signal profile data, the computer system comprising:

one or more processors;

storage media for storing a computer database;

a program module, executable by said one or more processors, for processing said biological signal profile data, said program module comprising;

instructions for receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in computer readable form in said computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

instructions for retrieving, from said computer database, a plurality of similarity metrics stored in computer readable form in said computer database, each similarity metric in said plurality of similarity metrics having been computed between (i) data points of said query profile, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile, thereby processing biological signal profile data.

53. The computer system of claim 7 or 13, wherein said program module further comprises instructions for user directed selection of the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics are computed.

82. The computer system of claim 13 wherein at least one biological signal profile used by said instructions for computing said plurality of similarity metrics comprises data points measured in response to a perturbation to a cell or an organism.

14. A computer network for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, the computer network comprising:

a first computer and a second computer; and

a data network coupled to said first and said second computer;

said first computer comprising;

a first processor;

a first storage media for storing a computer database;

a first program module, executable by said first processor, said first program module comprising;

instructions for storing a plurality of biological signal profiles in computer readable form in said computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent; and

instructions for receiving a command from said user to initiate a comparison algorithm, said command identifying a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

said second computer comprising;

a second processor;

a second program module, executable by said second processor, said second

program module comprising;

instructions for computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile.

27. The computer network of claim 14, 15, or 16, wherein each said similarity metric in said plurality of similarity metrics consists of a single scalar correlation coefficient.

28. The computer network of claim 14, 15, or 16, wherein each said similarity metric in said plurality of similarity metrics consists of a multidimensional correlation matrix.

29. The computer network of claim 14, 15, or 16, said first program module further comprising instructions for storing said plurality of similarity metrics in said database.

30. The computer network of claim 14, said first program module further comprising instructions for user directed selection of the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics is computed.

32. The computer network of claim 14, 15, or 16, wherein said instructions for receiving said command comprises instructions for selecting said query profile.

33. The computer network of claim 14, 15, or 16, wherein said plurality of biological signal profiles comprise gene expression level data.

34. The computer network of claim 14, 15, or 16, wherein said plurality of biological signal profiles comprise protein expression level data.

83. The computer network of claims 14, 15 or 16, wherein at least one biological signal profile used by said instructions for computing said plurality of similarity

15. A computer network for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, the computer network comprising:

a first computer and a second computer; and

a data network coupled to said first and said second computer;

said first computer comprising;

a first processor;

a first storage media for storing said computer database;

a first program module, executable by said first processor, said first program module comprising;

instructions for storing a plurality of biological signal profiles in said computer database in computer readable form, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent;

instructions for receiving a command from said user to initiate a comparison algorithm, said command identifying a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

instructions for retrieving from said computer database a plurality of similarity metrics, each similarity metric in said plurality of similarity metrics having been computed in accordance with said comparison algorithm between said query profile and a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile; and

said second computer comprising;

a second processor;

a second program module, executable by said second processor, said second program module comprising;

instructions for computing said plurality of similarity metrics; and

instructions for storing said plurality of similarity metrics in said computer database in computer readable form.

31. The computer network of claim 15, said first program module further comprising instructions for user directed selection of the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics is computed.

16. A computer network for processing biological signal profile data, the computer network comprising:

a first computer and a second computer; and

a data network coupled to said first and said second computer;

said first computer comprising;

a first processor;

a first storage media for storing a computer database;

a first program module, executable by said first processor, for processing said biological signal profile data, said first program module comprising;

instructions for receiving a command from a user to initiate a comparison algorithm, said command identifying a query profile selected from among a plurality of biological signal profiles stored in computer readable form in said computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent; and

said second computer comprising;

a second processor;

a second program module, executable by said second processor, said second program module comprising instructions for computing said plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

said first program module further comprising;

instructions for communicating as an ordered list said plurality of similarity metrics or said different target profiles represented by said plurality of similarity metrics, said plurality of similarity metrics or said different target profiles in said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile.

17. A method of using a computer network for processing biological signal profile data for storage in a computer database and for retrieval therefrom by a user, the method comprising:

storing a plurality of biological signal profiles in computer readable form in said computer database, each said biological signal profile in said plurality of biological signal profiles comprising a plurality of data points, each data point being a measurement of a level of a cellular constituent; and

receiving a command from said user to initiate a comparison algorithm, said command identifying a query profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database;

computing a plurality of similarity metrics, each similarity metric being computed in accordance with said comparison algorithm, between (i) data points of said query profile, and (ii) corresponding data points of a different target profile selected from among said plurality of biological signal profiles stored in computer readable form in said computer database; and

communicating as an ordered list said plurality of similarity metrics or said different target profiles, said ordered list being ordered by degree of correlation between said data points of said query profile and said corresponding data points of each said different target profile.

63. The method of claim 17, wherein each said similarity metric in said plurality of similarity metrics consists of a single scalar correlation coefficient.

64. The method of claim 17, wherein each said similarity metric in said plurality of similarity metrics consists of a multidimensional correlation matrix.

65. The method of claim 17, further comprising storing each said similarity metric in said plurality of similarity metrics in said computer database.

66. The method of claim 17, further comprising a step of selecting the data points of said query profile and the data points of each said different target profile between which said plurality of similarity metrics is computed.

67. The method of claim 17, wherein said step of receiving said command comprises a step of selecting said query profile.

68. The method of claim 17, wherein said plurality of biological signal profiles comprise gene expression level data.

69. The method claim 17, wherein said plurality of biological signal profiles comprise protein expression level data.