SYSTEMS AND METHODS FOR BIOCHEMICAL DATA ANALYSIS

• US 20130080373A1
• Filed: 09/24/2012
• Published: 03/28/2013
• Est. Priority Date: 09/22/2011
• Status: Active Grant

• Current Assignee: Bio-Rad Laboratories Incorporated
• Original Assignee: Bio-Rad Laboratories Incorporated
• Inventors: Thomsen, Niels Kirk, Dunaway, John Clopton, Yeck, Todd
• Granted Patent: US 9,792,548 B2
• Time in Patent Office: Days
• US Class Current: 706/50
• 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

one or more 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;

receiving a selection of a compare field from the plurality of first fields;

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

receiving a selection of an analyte from the one or more second fields for statistical analysis; and

providing a display of information separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field.

2. 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.

3. The method of claim 1, further comprising:

receiving a selection of a control group from a control group list; and

providing a visual indication on the display of statistical information as to which subgroup corresponds to the control group.

4. The method of claim 3, further comprising:

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.

5. The method of claim 3, 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.

6. 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.

7. The method of claim 6, further comprising:

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

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

filtering the subgroups of data for statistical analysis based on the selected filtering criteria.

8. The method of claim 6, 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.

9. The method of claim 6, wherein the first filter parameter is not the compare field.

10. The method of claim 1, 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.

11. The method of claim 10, further comprising:

displaying a list of analytes in a table,

wherein receiving a selection of an analyte from the one or more second fields for statistical analysis includes receiving a selection of an analyte in the table, and

wherein the one or more statistical values are displayed in the table in one or more cells corresponding to the selected analyte.

12. The method of claim 1, 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.

13. The method of claim 1, wherein at least one of the one or more second fields corresponds to a cell type as the respective analyte.

14. A computer program product comprising a tangible 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

one or more 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;

receiving a selection of a compare field from the plurality of first fields;

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

receiving a selection of an analyte from the one or more second fields for statistical analysis; and

providing a display of information separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field.

15. The computer program product of claim 14, wherein the instructions further comprise:

receiving a selection of a control group from a control group list; and

providing a visual indication on the display of statistical information as to which subgroup corresponds to the control group.

16. The computer program product of claim 14, 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.

17. The computer program product of claim 16, further comprising:

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

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

filtering the subgroups of data for statistical analysis based on the selected filtering criteria.

18. 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

one or more 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;

receive a selection of a compare field from the plurality of first fields;

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

receive a selection of an analyte from the one or more second fields for statistical analysis; and

provide a display of information separated by subgroups to convey statistical information for the selected analyte for each subgroup of the compare field.

19. The system of claim 18, wherein the one or more processors are further configured to:

receive a selection of a control group from a control group list; and

provide a visual indication on the display of statistical information as to which subgroup corresponds to the control group.

20. The system of claim 18, 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.

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

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

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

filter the subgroups of data for statistical analysis based on the selected filtering criteria.