Minimization of epigenetic surprisal data of epigenetic data within a time series

• US 9,002,888 B2
• Filed: 06/29/2012
• Issued: 04/07/2015
• Est. Priority Date: 06/29/2012
• Status: Active Grant

• Current Assignee: International Business Machines Corporation
• Original Assignee: International Business Machines Corporation
• Inventors: Friedlander, Robert R., Kraemer, James R.
• Primary Examiner(s): Beausoliel, Jr., Robert
• Assistant Examiner(s): BOWEN, RICHARD L
• Application Number:
  US13/537,385
• Publication Number:
  US 20140006365A1
• Time in Patent Office: 1,012 Days
• Field of Search: None
• US Class Current: 707/776
• CPC Class Codes: G06F 16/951 Indexing; Web crawling techniques
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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

Abstract

A method, computer program product and system of minimizing epigenetic surprisal data either by comparing epigenetic surprisal data to a fixed baseline epigenetic data, so that all of the comparisons were made to the same baseline epigenetic data or by comparing epigenetic surprisal data to a rolling baseline of epigenetic surprisal data—that is, after each comparison the baseline is changed to the data from the time point which had been compared previously.

Claims

1. A method of minimizing epigenetic surprisal data comprising:

a computer receiving a request for an epigenetic time series analysis comprising at least an indication of a baseline epigenetic surprisal data and a time period for the epigenetic time series analysis;

the computer retrieving a baseline epigenetic surprisal data and epigenetic surprisal data for at least one time point within the time period from a repository; and

the computer comparing the at least one epigenetic surprisal data comprising a location of an epigenetic modification, a time in which the epigenetic modification was collected and a type of epigenetic modification for the at least one time point within the time period to the baseline epigenetic surprisal data comprising a location of an epigenetic modification, a time in which the epigenetic modification was collected and a type of epigenetic modification, producing at least one epigenetic modification difference;

the computer storing the at least one epigenetic modification difference in a repository; and

repeating the method for all epigenetic surprisal data time points within the time period.

2. The method of claim 1, further comprising a computer recreating an epigenetic map of an organism at a specific time point within the time period by:

retrieving an epigenetic surprisal data within the time period from the repository;

retrieving baseline epigenetic surprisal data from the repository; and

altering the baseline epigenetic surprisal data based on the epigenetic surprisal data at a specific time point by altering the map to include epigenetic modifications specified by the epigenetic surprisal data associated with a location;

resulting in an entire epigenetic map of an organism at a specific time point within the time period.

3. The method of claim 1, further comprising prior to the computer receiving a request for an epigenetic time series analysis, the computer:

receiving an epigenetic map at time x of an organism comprising epigenetic modifications;

comparing the epigenetic map at time x to a reference epigenetic map, to find differences where epigenetic modifications of the organism at time x which are different from the epigenetic modifications of the reference epigenetic map; and

the computer using the differences to create and store epigenetic surprisal data in a repository.

4. The method of claim 1, wherein the organism is an animal.

5. The method of claim 1, wherein the organism is a microorganism.

6. The method of claim 1, wherein the organism is a plant.

7. The method of claim 1, wherein the organism is a fungus.

8. The method of claim 1, wherein the epigenetic modification is generated by storing only differences between an epigenetic map at time x and a reference epigenetic map.

9. A method of minimizing epigenetic surprisal data comprising:

a computer receiving a request for an epigenetic time series analysis comprising at least a a time period for the epigenetic time series analysis;

the computer retrieving epigenetic surprisal data at time points within the time period from a repository, the epigenetic surprisal data comprising a location of an epigenetic modification, a time in which the epigenetic modification was collected and a type of epigenetic modification;

the computer designating a first epigenetic surprisal data at a time point within the time period as a baseline;

the computer comparing the baseline comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification to a next epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification and storing the difference in a repository as epigenetic surprisal data representative of the comparison of the baseline to the next epigenetic surprisal data;

the computer designating the next epigenetic surprisal data from the comparison as the baseline, and

the computer repeating the step of comparing and designating, until all epigenetic data in the time period have been compared.

10. The method of claim 9, further comprising a computer recreating an epigenetic map of an organism at a specific time point within the time period by:

retrieving an epigenetic surprisal data within the time period from the repository;

retrieving baseline epigenetic surprisal data from the repository; and

altering the baseline epigenetic surprisal data based on the epigenetic surprisal data at a specific time point by altering the epigenetic map to include epigenetic modifications specified by the epigenetic surprisal data associated with a location;

resulting in an entire epigenetic map of an organism at a specific time point within the time period.

11. The method of claim 9, further comprising prior to the computer receiving a request for an epigenetic time series analysis, the computer:

receiving an epigenetic map at time x of an organism comprising epigenetic modifications;

comparing the epigenetic map at time x to a reference epigenetic map, to find differences where epigenetic modifications of the organism at time x which are different from the epigenetic modifications of the reference epigenetic map; and

the computer using the differences to create and store epigenetic surprisal data in a repository.

12. The method of claim 9, wherein the organism is an animal.

13. The method of claim 9, wherein the organism is a microorganism.

14. The method of claim 9, wherein the organism is a plant.

15. The method of claim 9, wherein the organism is a fungus.

16. A computer program product for minimizing epigenetic surprisal data, comprising:

one or more computer-readable storage mediums;

program instructions, stored on at least one of the one or more storage mediums, to receive a request for an epigenetic time series analysis comprising at least an indication of a baseline epigenetic surprisal data and a time period for the epigenetic time series analysis;

program instructions, stored on at least one of the one or more storage mediums, to retrieve a baseline epigenetic surprisal data and epigenetic surprisal data for at least one time point within the time period from a repository;

program instructions, stored on at least one of the one or more storage mediums, to compare the at least one epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification within the time period to the baseline epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification, producing at least one epigenetic modification difference;

program instructions, stored on at least one of the one or more storage mediums, to store the at least one epigenetic modification difference in a repository; and

program instructions, stored on at least one of the one or more storage mediums, to repeat the method for all epigenetic surprisal data time points within the time period.

17. The computer program product of claim 16, further comprising program instructions, stored on at least one of the one or more storage mediums, to recreate an epigenetic map of an organism at a specific time point within the time period by:

retrieving an epigenetic surprisal data within the time period from the repository;

retrieving baseline epigenetic surprisal data from the repository; and

altering the baseline epigenetic surprisal data based on the epigenetic surprisal data at a specific time point by altering the map to include epigenetic modifications specified by the epigenetic surprisal data associated with a location;

resulting in an entire epigenetic map of an organism at a specific time point within the time period.

18. The computer program product of claim 16, further comprising prior to the program instructions, stored on at least one of the one or more storage mediums, to receive a request for an epigenetic time series analysis, the computer:

receiving an epigenetic map at time x of an organism comprising epigenetic modifications;

comparing the epigenetic map at time x to a reference epigenetic map, to find differences where epigenetic modifications of the organism at time x which are different from the epigenetic modifications of the reference epigenetic map; and

the computer using the differences to create and store epigenetic surprisal data in a repository.

19. The computer program product of claim 16, wherein the organism is an animal.

20. The computer program product of claim 16, wherein the organism is a microorganism.

21. The computer program product of claim 16, wherein the organism is a plant.

22. The computer program product of claim 16, wherein the organism is a fungus.

23. The computer program product of claim 16, wherein the epigenetic modification is generated by storing only differences between an epigenetic map at time x and a reference epigenetic map.

24. A computer program product for minimizing epigenetic surprisal data, comprising:

one or more computer-readable, storage mediums;

program instructions, stored on at least one of the one or more storage mediums, to receive a request for an epigenetic time series analysis comprising at least a time period for the epigenetic time series analysis;

program instructions, stored on at least one of the one or more storage mediums, to retrieve epigenetic surprisal data at time points within the time period from a repository;

program instructions, stored on at least one of the one or more storage mediums, to designate a first epigenetic surprisal data at a time point within the time period as a baseline;

program instructions, stored on at least one of the one or more storage mediums, to compare the baseline comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification to a next epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification and storing the difference in a repository as epigenetic surprisal data representative of the comparison of the baseline to the next epigenetic surprisal data;

program instructions, stored on at least one of the one or more storage mediums, to designate the next epigenetic surprisal data from the comparison as the baseline, and

the program instructions, stored on at least one of the one or more storage mediums, to repeat the step of comparing and designating, until all epigenetic surprisal data in the time period have been compared.

25. The computer program product of claim 24, further comprising program instructions, stored on at least one of the one or more storage mediums, to recreate an epigenetic map of an organism at a specific time point within the time period by:

retrieving an epigenetic surprisal data within the time period from the repository;

retrieving baseline epigenetic surprisal data from the repository; and

altering the baseline epigenetic surprisal data based on the epigenetic surprisal data at a specific time point by altering the map to include epigenetic modifications specified by the epigenetic surprisal data associated with a location;

resulting in an entire epigenetic map of an organism at a specific time point within the time period.

26. The computer program product of claim 24, further comprising prior to the program instructions, stored on at least one of the one or more storage mediums, to receive a request for an epigenetic time series analysis, the computer:

receiving an epigenetic map at time x of an organism comprising epigenetic modifications;

comparing the epigenetic map at time x to a reference epigenetic map, to find differences where epigenetic modifications of the organism at time x which are different from the epigenetic modifications of the reference epigenetic map; and

the computer using the differences to create and store epigenetic surprisal data in a repository.

27. The computer program product of claim 24, wherein the organism is an animal.

28. The computer program product of claim 24, wherein the organism is a microorganism.

29. The computer program product of claim 24, wherein the organism is a plant.

30. The computer program product of claim 24, wherein the organism is a fungus.

31. A computer system for minimizing surprisal data comprising:

one or more processors, one or more computer-readable memories and one or more computer-readable, storage mediums;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to receive a request for an epigenetic time series analysis comprising at least an indication of a baseline epigenetic surprisal data and a time period for the epigenetic time series analysis;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to retrieve a baseline epigenetic surprisal data and epigenetic surprisal data for at least one time point within the time period from a repository;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to compare the at least one epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification within the time period to the baseline epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification, producing at least one epigenetic modification difference;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to store the at least one epigenetic modification difference in a repository; and

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to repeat the method for all epigenetic surprisal data time points within the time period.

32. The computer system of claim 31, further comprising program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to recreate an epigenetic map of an organism at a specific time point within the time period by:

retrieving an epigenetic surprisal data within the time period from the repository;

retrieving baseline epigenetic surprisal data from the repository; and

altering the baseline epigenetic surprisal data based on the epigenetic surprisal data at a specific time point by altering the map to include epigenetic modifications specified by the epigenetic surprisal data associated with a location;

resulting in an entire epigenetic map of an organism at a specific time point within the time period.

33. The computer system of claim 31, further comprising prior to the program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to receive a request for an epigenetic time series analysis, the computer:

receiving an epigenetic map at time x of an organism comprising epigenetic modifications;

comparing the epigenetic map at time x to a reference epigenetic map, to find differences where epigenetic modifications of the organism at time x which are different from the epigenetic modifications of the reference epigenetic map; and

the computer using the differences to create and store epigenetic surprisal data in a repository.

34. The computer system of claim 31, wherein the organism is an animal.

35. The computer system of claim 31, wherein the organism is a microorganism.

36. The computer system of claim 31, wherein the organism is a plant.

37. The computer system of claim 31, wherein the organism is a fungus.

38. The computer system of claim 31, wherein the epigenetic modification is generated by storing only differences between an epigenetic map at time x and a reference epigenetic map.

39. A computer system for minimizing epigenetic surprisal data, comprising:

one or more processors, one or more computer-readable memories and one or more computer-readable, storage mediums;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to a receive a request for an epigenetic time series analysis comprising at least a time period for the epigenetic time series analysis;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to retrieve epigenetic surprisal data at time points within the time period from a repository, the epigenetic surprisal data comprising a location of an epigenetic modification, a time in which the epigenetic modification was collected and a type of epigenetic modification;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to designate a first epigenetic surprisal data at a time point within the time period as a baseline;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to compare the baseline comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification to a next epigenetic surprisal data comprising a location of the epigenetic modification, the time in which the epigenetic modification was collected and the type of epigenetic modification and storing the difference in a repository as epigenetic surprisal data representative of the comparison of the baseline to the next epigenetic surprisal data;

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to designate the next epigenetic surprisal data from the comparison as the baseline, and

program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to repeat the step of comparing and designating, until all epigenetic data in the time period have been compared.

40. The computer system of claim 39, further comprising program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to recreate an epigenetic map of an organism at a specific time point within the time period by:

retrieving an epigenetic surprisal data within the time period from the repository;

retrieving baseline epigenetic surprisal data from the repository; and

altering the baseline epigenetic surprisal data based on the epigenetic surprisal data at a specific time point by altering the map to include epigenetic modifications specified by the epigenetic surprisal data associated with a location;

resulting in an entire epigenetic map of an organism at a specific time point within the time period.

41. The computer system of claim 39, further comprising prior to the program instructions, stored on at least one of the one or more storage mediums for execution by at least one of the one or more processors via at least one of the one or more memories, to receive a request for an epigenetic time series analysis, the computer:

receiving an epigenetic map at time x of an organism comprising epigenetic modifications;

comparing the epigenetic map at time x to a reference epigenetic map, to find differences where epigenetic modifications of the organism at time x which are different from the epigenetic modifications of the reference epigenetic map; and

the computer using the differences to create and store epigenetic surprisal data in a repository.

42. The computer system of claim 39, wherein the organism is an animal.

43. The computer system of claim 39, wherein the organism is a microorganism.

44. The computer system of claim 39, wherein the organism is a plant.

45. The computer system of claim 39, wherein the organism is a fungus.