Systems and methods for biochemical data analysis

• US 9,792,548 B2
• Filed: 09/24/2012
• Issued: 10/17/2017
• Est. Priority Date: 09/22/2011
• Status: Active Grant

• Current Assignee: Bio-Rad Laboratories Incorporated
• Original Assignee: Bio-Rad Laboratories Incorporated
• Inventors: Yeck, Todd, Thomsen, Niels Kirk, Dunaway, John Clopton
• Primary Examiner(s): Borin, Michael
• Application Number:
  US13/625,753
• Publication Number:
  US 20130080373A1
• Time in Patent Office: 1,849 Days
• Field of Search: None
• CPC Class Codes: G06N 5/02 Knowledge representation; Symbolic representation
• 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 50/30 Data warehousing; Computing architectures

Abstract

Methods and systems for biochemical data analysis are provided. A dataset can be received and a selection of a compare field can be used for creation of sub-groups of data to run statistical analysis on. The sub-groups of the dataset can be created based on the selection of the compare field. Statistical information about each sub-group of data can be calculated and displayed on a user display. Other information can be provided for further dataset refinements. A user may supply a control group selection, and such a selection may then result in an indication on the display of which population represents the control group. A user may supply information for further dataset filtering. Such information may be used to filter data, prior to creating the sub-groups for statistical analysis.

Claims

1. A method of biochemical data analysis, the method comprising:

receiving, at a computer system, a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populating a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

displaying, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receiving, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identifying a plurality of values in the database for the selected compare field;

identifying, by the computer system, subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically displaying, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receiving, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieving a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically displaying, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receiving, at the GUI page, a selection of a control group from a control group list, wherein the user uses the input device to select the control group; and

in response to the user selecting the control group, automatically displaying, on the display of the computer system, a visual indication as to which subgroup corresponds to the control group.

2. The method of claim 1, further comprising:

in response to the user selecting the compare field, automatically updating the control group list based on the selection of the compare field, wherein the control group represents a particular data value from the plurality of values of the compare field.

3. The method of claim 1, wherein the display of statistical information includes a series of graphs, each graph corresponding to a different subgroup, and wherein the visual indication includes displaying the graph corresponding to the control group in a left justified manner.

4. The method of claim 1, further comprising:

receiving a selection of a first filter parameter from a filter parameter list, wherein the filter parameter list includes at least a portion of the plurality of first fields, the first filter parameter having a plurality of first criteria values;

receiving a selection of a portion of the plurality of first criteria values; and

displaying statistical information corresponding to the selected portion and not to the non-selected first criteria values.

5. The method of claim 1, wherein providing a display of information separated by subgroups includes:

displaying a graph for each subgroup, wherein each graph displays each concentration of the subgroup along an axis of concentration value.

6. The method of claim 1, further comprising:

receiving, at the GUI page, a selection of a second analyte from the list of the plurality of second fields for statistical analysis, wherein the user uses the input device to select the second analyte;

in response to the user selecting the second analyte, retrieving a plurality of second concentrations of the selected second analyte from the dataset; and

in response to the user selecting the second analyte, automatically updating the display of the computer system to display information of the retrieved plurality of second concentrations separated by subgroups to convey statistical information for the selected second analyte for each subgroup of the compare field.

7. The method of claim 1, wherein the input device is a mouse.

8. The method of claim 1, wherein the display of the computer system is a monitor.

9. The method of claim 2, wherein the control group list includes all unique possible data values for the selected compare field.

10. A method of biochemical data analysis, the method comprising:

receiving, at a computer system, a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populating a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

displaying, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receiving, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identifying a plurality of values in the database for the selected compare field;

identifying, by the computer system, subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically displaying, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receiving, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieving a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically displaying, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receiving, at the GUI page, a selection of a first filter parameter from a filter parameter list, wherein the filter parameter list includes at least a portion of the plurality of first fields, the first filter parameter having a plurality of first criteria values;

receiving, at the GUI page, a selection of a portion of the plurality of first criteria values;

in response to the user selecting the portion, automatically displaying, on the display of the computer system, statistical information corresponding to the selected portion and not to the non-selected first criteria values;

refreshing a user view of possible criteria values based on the selected first filter parameter, wherein the possible criteria values allow filtering of data on which a statistical analysis is performed;

receiving, at the GUI page, one or more user selections of criteria values based on the refreshed user view; and

in response to the user selecting the criteria values, automatically filtering the subgroups of data for statistical analysis based on the selected filtering criteria.

11. The method of claim 10, further comprising:

receiving a selection of a second filter parameter from the filter parameter list, the second filter parameter having a plurality of second criteria values;

receiving a selection of a portion of the plurality of second criteria values; and

displaying statistical information corresponding to the selected portion of the first and second criteria values and not to the non-selected first and second criteria values.

12. The method of claim 10, wherein the first filter parameter is not the compare field.

13. The method of claim 10, further comprising:

receiving a selection of a type of statistical analysis;

calculating one or more statistical values for the data corresponding to the selected analyte based on the received type of statistical analysis; and

displaying the one or more statistical values.

14. A method of biochemical data analysis, the method comprising:

receiving, at a computer system, a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populating a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

displaying, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receiving, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identifying a plurality of values in the database for the selected compare field;

identifying, by the computer system, subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically displaying, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receiving, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieving a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically displaying, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receiving, at the GUI page, a selection of a type of statistical analysis;

in response to the user selecting the type of statistical analysis, automatically calculating one or more statistical values for the data corresponding to the selected analyte based on the received type of statistical analysis; and

displaying, on the display of the computer system, the one or more statistical values in the table in one or more cells corresponding to the selected analyte.

15. The method of claim 14, further comprising:

receiving a definition of a custom attribute for the dataset for the plurality of biological samples, wherein the custom attribute is a user-supplied attribute that corresponds to one of the plurality of first fields.

16. The method of claim 14, wherein at least one of the plurality of second fields corresponds to a cell type as the respective analyte.

17. A computer program product comprising a tangible non-transitory computer readable medium storing a plurality of instructions for controlling a computer system to perform an operation for biochemical data analysis, the instructions comprising:

receiving a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populating a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

displaying, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receiving, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identifying a plurality of values in the database for the selected compare field;

identifying subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically displaying, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receiving, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieving a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically displaying, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receiving, at the GUI page, a selection of a control group from a control group list, wherein the user uses the input device to select the control group; and

in response to the user selecting the control group, automatically displaying, on the display of the computer system, a visual indication as to which subgroup corresponds to the control group.

18. The computer program product of claim 17, wherein the instructions further comprise:

receiving a selection of a first filter parameter from a filter parameter list, wherein the filter parameter list includes at least a portion of the plurality of first fields, the first filter parameter having a plurality of first criteria values;

receiving a selection of a portion of the plurality of first criteria values; and

displaying statistical information corresponding to the selected portion and not to the non-selected first criteria values.

19. A computer program product comprising a tangible non-transitory computer readable medium storing a plurality of instructions for controlling a computer system to perform an operation for biochemical data analysis, the instructions comprising:

receiving a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populating a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

displaying, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receiving, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identifying a plurality of values in the database for the selected compare field;

identifying subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically displaying, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receiving, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieving a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically displaying, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receiving, at the GUI page, a selection of a first filter parameter from a filter parameter list, wherein the filter parameter list includes at least a portion of the plurality of first fields, the first filter parameter having a plurality of first criteria values;

receiving, at the GUI page, a selection of a portion of the plurality of first criteria values;

in response to the user selecting the portion, automatically displaying, on the display of the computer system, statistical information corresponding to the selected portion and not to the non-selected first criteria values;

refreshing a user view of possible criteria values based on the selected first filter parameter, wherein the possible criteria values allow filtering of data on which a statistical analysis is performed;

receiving, at the GUI page, one or more user selections of criteria values based on the refreshed user view; and

in response to the user selecting the criteria values, automatically filtering the subgroups of data for statistical analysis based on the selected filtering criteria.

20. A system for biochemical data analysis comprising:

a database system; and

one or more processors configured to;

receive a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populate a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

display, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receive, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identify a plurality of values in the database for the selected compare field;

identify subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically display, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receive, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieve a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically display, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receive, at the GUI page, a selection of a control group from a control group list, wherein the user uses the input device to select the control group; and

in response to the user selecting the control group, automatically display, on the display of the computer system, a visual indication as to which subgroup corresponds to the control group.

21. The system of claim 20, wherein the one or more processors are further configured to:

receive a selection of a first filter parameter from a filter parameter list, wherein the filter parameter list includes at least a portion of the plurality of first fields, the first filter parameter having a plurality of first criteria values;

receive a selection of a portion of the plurality of first criteria values; and

display statistical information corresponding to the selected portion and not to the non-selected first criteria values.

22. A system for biochemical data analysis comprising:

a database system; and

one or more processors configured to;

receive a dataset for a plurality of biological samples, the dataset having a plurality of fields for each biological sample, at least a portion of the dataset being obtained from experiments involving the biological samples, wherein the dataset includes;

a plurality of first fields, each first field including a plurality of values, each value corresponding to a respective characteristic of a respective biological sample, and

a plurality of second fields, each second field corresponding to a respective analyte and including a plurality of concentrations of the respective analyte in the experiments, each concentration corresponding to a respective biological sample;

in response to a user selecting the dataset via a graphical user interface (GUI) page of the computer system, automatically populate a drop-down box of the GUI page with the plurality of first fields, wherein the user uses an input device to select the dataset in the GUI page;

display, on a display of the computer system, a list of the plurality of first fields in a first region of the GUI page in response to the user selecting the drop-down box in the GUI page, wherein the user uses the input device to select the drop-down box;

receive, at the GUI page, a selection of a compare field from the list of the plurality of first fields, wherein the user uses the input device to select the compare field;

in response to the user selecting the compare field, automatically identify a plurality of values in the database for the selected compare field;

identify subgroups of the biological samples in the dataset for statistical analysis based on the identified plurality of values for the selected compare field, wherein biological samples of a subgroup have a same value for the compare field;

in further response to the user selecting the dataset, automatically display, on the display of the computer system, a list of the plurality of second fields in a second region of the GUI page;

receive, at the GUI page, a selection of an analyte from the list of the plurality of second fields displayed on the display of the computer system for statistical analysis, wherein the user uses the input device to select the analyte;

in response to the user selecting the analyte, retrieve a plurality of concentrations of the selected analyte from the dataset;

in response to the user selecting the analyte and the compare field, automatically display, on the display of the computer system, information of the retrieved plurality of concentrations separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field, wherein the information of the retrieved plurality of concentrations separated by subgroups is displayed within a third region of the GUI page to facilitate visual comparison;

receive, at the GUI page, a selection of a first filter parameter from a filter parameter list, wherein the filter parameter list includes at least a portion of the plurality of first fields, the first filter parameter having a plurality of first criteria values;

receive, at the GUI page, a selection of a portion of the plurality of first criteria values;

in response to the user selecting the portion, automatically display, on the display of the computer system, statistical information corresponding to the selected portion and not to the non-selected first criteria values;

refresh a user view of possible criteria values based on the selected first filter parameter, wherein the possible criteria values allow filtering of data on which a statistical analysis is performed;

receive, at the GUI page, one or more user selections of criteria values based on the refreshed user view; and

in response to the user selecting the criteria values, automatically filter the subgroups of data for statistical analysis based on the selected filtering criteria.