Method, apparatus and computer program product for metabolomics analysis
A method is provided for analyzing metabolite data in a sample, comprising analyzing a sample to determine a first number of metabolites, and amount of each metabolite, included in the sample, and a second number of the first number of metabolites that are regulated. Biochemical pathways are determined, each having a third number of the first number of metabolites that are included in the sample and in the determined biochemical pathway. For each of the determined biochemical pathways having the third number of metabolites, a fourth number of the second number of metabolites that are included in the sample and in the determined biochemical pathway that are regulated metabolites is determined. Each of the third number of metabolites within one of the determined biochemical pathways is displayed and distinguished by the amount of each corresponding metabolite included in the sample. An associated apparatus and computer program product are also provided.
1. A method of analyzing metabolomics data for a sample to detect a plurality of metabolites in the sample, comprising:
inputting into a user interface one or more selected attributes associated with the sample;
analyzing the metabolomics data based on the one or more selected attributes to detect a first number of metabolites, and the amount of each metabolite, present in the sample;
detecting a second number of metabolites, corresponding to one or more regulated metabolites present in the first number of metabolites;
detecting a third number of metabolites present in the first number of metabolites and present in each of one or more biochemical pathways associated with the sample;
for each of the one or more biochemical pathways having the third number of metabolites, detecting a fourth number of metabolites, corresponding to regulated metabolites present in the sample and in the respective biochemical pathway;
diagnosing a significance of the third number of metabolites in each of the one or more biochemical pathways, as indicated by a category enrichment ratio associated therewith, by:
distinguishing each of the third number of metabolites within one of the one or more biochemical pathways, on a display, by the amount of each corresponding metabolite detected in the sample;
determining a category enrichment ratio for each of the one or more biochemical pathways, by determining a pathway enrichment ratio between a first quotient and a second quotient, the first quotient being between the fourth number of the metabolites and a total number of metabolites included in the respective biochemical pathway, and the second quotient being between the second number of metabolites and the first number of metabolites in the sample;
ranking the one or more biochemical pathways by their category enrichment ratio;
displaying an indicium of each of the one or more ranked biochemical pathways on the display such that the indicia of the ranked one or more biochemical pathways are distinguished from each other;
allowing the user to vary the one or more selected attributes inputted into the user interface;
automatically re-ranking the one or more biochemical pathways in response to the varying of the one or more selected attributes by the user; and
displaying a new distinguishing indicium of each of the one or more re-ranked biochemical pathways.
2. The method of claim 1 , wherein each displayed indicium represents a magnitude of the category enrichment ratio for each biochemical pathway.
3. The method of claim 2 , wherein the indicia are distinguished by a color, a color gradation, or a font.
4. The method of claim 1 , wherein distinguishing each of the third number of metabolites within the one of the one or more biochemical pathways comprises distinguishing each of the third number of metabolites within the one of the one or more biochemical pathways according to the ranking of the category enrichment ratio thereof.
5. The method of claim 1 , wherein each metabolite in the sample is represented as a node within the one or more biochemical pathways, and distinguishing each of the third number of metabolites within the one of the one or more biochemical pathways by the amount of each corresponding metabolite detected in the sample further comprises distinguishing the metabolites in the sample by varying a size, color, or color gradation of each node in the one of the one or more biochemical pathways displayed on the display in accordance with the amount of each corresponding metabolite detected in the sample.
6. The method of claim 5 , further comprising annotating each node with actual data for the metabolite from the analysis of the sample, or previously known characterization data associated with the metabolite.
7. The method of claim 6 , further comprising displaying the annotation associated with the node upon selection thereof on the displayed one of the one or more biochemical pathways.
8. An apparatus for analyzing metabolomics data for a sample to detect a plurality of metabolites in the sample, comprising:
a processor configured to control a device to at least:
analyze the metabolomics data based on one or more selected attributes to detect a first number of metabolites, and the amount of each metabolite, present in the sample;
detect a second number of metabolites, corresponding to one or more regulated metabolites present in the first number of metabolites;
detect a third number of metabolites present in the first number of metabolites and present in each of one or more biochemical pathways associated with the sample;
for each of the one or more biochemical pathways having the third number of metabolites, detect a fourth number of metabolites, corresponding to regulated metabolites present in the sample and in the respective biochemical pathway; and
diagnose a significance of the third number of metabolites in each of the one or more biochemical pathways, as indicated by a category enrichment ratio associated therewith, by:
distinguishing each of the third number of metabolites within one of the one or more biochemical pathways, on a display, according to the amount of each corresponding metabolite detected in the sample;
determining a category enrichment ratio for each of the one or more biochemical pathways, by determining a pathway enrichment ratio between a first quotient and a second quotient, the first quotient being between the fourth number of the metabolites and a total number of metabolites included in the respective biochemical pathway, and the second quotient being between the second number of metabolites and the first number of metabolites in the sample;
ranking the one or more biochemical pathways by their category enrichment ratio;
displaying an indicium of each of the one or more biochemical pathways on the display such that the indicia of the ranked one or more biochemical pathways are distinguished from each other; and
a user interface in communication with the processor and configured to have inputted therein the one or more selected attributes associated with the sample, the user interface being further configured to allow the user to vary the one or more selected attributes inputted into the user interface, and in response to the varying of the one or more selected attributes by the user, cause the processor to automatically re-rank the one or more biochemical pathways, and display a new distinguishing indicium of each of the one or more re-ranked biochemical pathways.
9. The apparatus of claim 8 , wherein the processor is further configured to control the device such that each displayed indicium represents a magnitude of the category enrichment ratio for each biochemical pathway.
10. The apparatus of claim 9 , wherein the processor is further configured associate a color, a color gradation, or a font with an indicium of each of the biochemical pathways.
11. The apparatus of claim 8 , wherein the processor is configured to control the device to distinguish each of the third number of metabolites within the one of the one or more biochemical pathways according to the ranking of the category enrichment ratio thereof.
12. The apparatus of claim 8 , wherein each metabolite in the sample is represented as a node within the one or more biochemical pathways, and wherein the processor is further configured to control the device to distinguish the metabolites in the sample by varying a size, color, or color gradation of each node in the one of the one or more biochemical pathways displayed on the display in accordance with the amount of each corresponding metabolite detected in the sample.
13. The apparatus of claim 12 , wherein the processor is further configured to control the device to annotate each node with actual data for the metabolite from the analysis of the sample, or previously known characterization data associated with the metabolite.
14. The apparatus of claim 13 , wherein the processor is further configured to control the device to display the annotation associated with the node upon selection thereof on the displayed one of the one or more biochemical pathways.
15. A computer program product comprising at least one non-transitory computer readable storage medium having computer program code stored thereon, the computer program code being configured to analyze metabolomics data for a sample to detect a plurality of metabolites in the sample, and comprising:
program code for receiving one or more selected attributes associated with the sample inputted into a user interface;
program code for analyzing the metabolomics data based on the one or more selected attributes to detect a first number of metabolites, and the amount of each metabolite, present in the sample;
program code for detecting a second number of metabolites, corresponding to one or more regulated metabolites present in the first number of metabolites;
program code for detecting a third number of metabolites present in the first number of metabolites and present in each of one or more biochemical pathways associated with the sample;
program code for detecting, for each of the one or more biochemical pathways having the third number of metabolites, a fourth number of metabolites, corresponding to regulated metabolites present in the sample and in the respective biochemical pathway;
program code for diagnosing a significance of the third number of metabolites in each of the one or more biochemical pathways, as indicated by a category enrichment ratio associated therewith, by:
distinguishing each of the third number of metabolites within one of the one or more biochemical pathways, on a display, according to the amount of each corresponding metabolite detected in the sample;
determining a category enrichment ratio for each of the one or more biochemical pathways, by determining a pathway enrichment ratio between a first quotient and a second quotient, the first quotient being between the fourth number of the metabolites and a total number of metabolites included in the respective biochemical pathway, and the second quotient being between the second number of metabolites and the first number of metabolites in the sample; and
ranking the one or more biochemical pathways by their category enrichment ratio;
displaying an indicium of each of the one or more ranked biochemical pathways on the display such that the indicia of the ranked one or more biochemical pathways are distinguished from each other; and
program code for allowing the user to vary the one or more selected attributes inputted into the user interface;
program code for automatically re-ranking the one or more biochemical pathways in response to the varying of the one or more selected attributes by the user
program code for displaying a new distinguishing indicium of each of the one or more re-ranked biochemical pathways.
16. The computer program product of claim 15 , wherein each displayed indicium represents a magnitude of the category enrichment ratio for each biochemical pathway.
17. The computer program product of claim 16 , wherein the program code further associates a color, a color gradation, or a font with an indicium of each of the biochemical pathways.
18. The computer program product of claim 15 , wherein the program code for distinguishing each of the third number of metabolites within the one of the one or more biochemical pathways comprises program code for distinguishing each of the third number of metabolites within the one of the one or more biochemical pathways according to the ranking of the category enrichment ratio thereof.
19. The computer program product of claim 15 , wherein each metabolite in the sample is represented as a node within the one or more biochemical pathways, and wherein the program code for distinguishing each of the third number of metabolites within one of the one or more biochemical pathways by the amount of each corresponding metabolite detected in the sample, further comprises program code for distinguishing the metabolites in the sample by varying a size, color, or color gradation of each node in the one of the one or more biochemical pathways displayed on the display in accordance with the amount of each corresponding metabolite detected in the sample.
20. The computer program product of claim 19 , further comprising program code for annotating each node with actual data for the metabolite from the analysis of the sample, or previously known characterization data associated with the metabolite.
21. The computer program product of claim 20 , further comprising program code for displaying the annotation associated with the node upon selection thereof on the displayed one of the one or more biochemical pathways.