Method and system for profiling biological systems

Abstract

The present invention provides methods and systems for developing profiles of a biological system based on the discernment of similarities, differences, and/or correlations between biomolecular components, of a single biomolecular component type, of a plurality of biological samples. Preferably, the method comprises utilizing hierarchical multivariate analysis of spectrometric data at one or more levels of correlation.

1 - 44 . (canceled)  
     
     
         45 . A method of profiling a state of a biological system in an animal, the method comprising the steps of: 
 (a) providing a plurality of data sets derived from a biological sample type, the plurality of data sets comprising different types of measurements of a sample of a biological system;    (b) preprocessing the plurality of the data sets to generate preprocessed data sets;    (c) evaluating the preprocessed data sets with a multivariate analysis and correlating features among the preprocessed data sets to determine one or more sets of differences among at least a portion of the plurality of data sets;    (d) generating a profile of one or more biomarkers in response to one or more correlations, the profile characterizing a state of the biological system; and    (e) displaying at least a portion of the data relevant to the profile.    
     
     
         46 . The method of  claim 45  wherein the step of preprocessing comprises the step of normalizing the plurality of the data sets.  
     
     
         47 . The method of  claim 45  wherein the step of preprocessing comprises the step of reducing the noise of the plurality of the data sets.  
     
     
         48 . The method of  claim 45  wherein the step of preprocessing comprises the step of applying a partial linear fit technique to the plurality of the data sets.  
     
     
         49 . The method of  claim 45 , wherein the plurality of data sets comprises different types of measurements of a biomolecule component type.  
     
     
         50 . The method of  claim 49 , wherein the biomolecule component type is a gene transcript, a protein, or a metabolite.  
     
     
         51 . The method of  claim 45 , wherein the different types of measurements comprise different types of spectrometric measurements.  
     
     
         52 . The method of  claim 51 , wherein the spectrometric measurements comprise data from different instrument configurations of the same spectrometric technique.  
     
     
         53 . The method of  claim 45 , wherein the biological sample type is selected from the group consisting of blood, blood plasma, blood serum, cerebrospinal fluid, bile, saliva, synovial fluid, pleural fluid, pericardial fluid, peritoneal fluid, feces, nasal fluid, ocular fluid, intracellular fluid, intercellular fluid, lymph fluid, and urine.  
     
     
         54 . The method of  claim 45 , wherein the biological sample type is selected from the group consisting of liver cells, epithelial cells, endothelial cells, kidney cells, prostate cells, blood cells, lung cells, brain cells, skin cells, adipose cells, tumor cells, and mammary cells.  
     
     
         55 . The method of  claim 45 , wherein the plurality of data sets is derived from one biological sample type.  
     
     
         56 . The method of  claim 45 , wherein the plurality of data sets is derived from one biological sample type that is treated differently.  
     
     
         57 . The method of  claim 45 , wherein the plurality of data sets are derived from biological samples taken at different times for the same organism.  
     
     
         58 . The method of  claim 45 , wherein the biological system is in a mammal.  
     
     
         59 . An article of manufacture having a computer-readable medium with computer-readable instructions embodied thereon for performing the method of  claim 45 .  
     
     
         60 . A method of profiling a state of a biological system of an animal, the method comprising the steps of: 
 (a) analyzing a sample of a biological system to provide a plurality of data sets, the plurality of data sets comprising different types of measurements of the sample of the biological system;    (b) preprocessing the plurality of data sets to generate preprocessed data sets;    (c) evaluating the preprocessed data sets with a multivariate analysis and correlating features among the plurality of the data sets to determine one or more sets of differences among at least a portion of the plurality of data sets; and    (d) generating a profile of one or more biomarkers in response to one or more correlations, the profile characterizing a state of the biological system.    
     
     
         61 . The method of  claim 60 , wherein the step of preprocessing comprises the step of normalizing the plurality of the data sets.  
     
     
         62 . The method of  claim 60 , wherein the step of preprocessing comprises the step of reducing the noise of the plurality of the data sets.  
     
     
         63 . The method of  claim 60 , wherein the step of preprocessing comprises the step of applying a partial linear fit technique to the plurality of the data sets.  
     
     
         64 . The method of  claim 60 , wherein the plurality of data sets comprises different types of measurements of a biomolecule component type.  
     
     
         65 . The method of  claim 64 , wherein the biomolecule component type is a gene transcript, a protein, or a metabolite.  
     
     
         66 . The method of  claim 60 , wherein the different types of measurements comprise different types of spectrometric measurements.  
     
     
         67 . The method of  claim 66 , wherein the spectrometric measurements comprise data from different instrument configurations of the same spectrometric technique.  
     
     
         68 . The method of  claim 60 , wherein the biological sample type is selected from the group consisting of blood, blood plasma, blood serum, cerebrospinal fluid, bile, saliva, synovial fluid, pleural fluid, pericardial fluid, peritoneal fluid, feces, nasal fluid, ocular fluid, intracellular fluid, intercellular fluid, lymph fluid, and urine.  
     
     
         69 . The method of  claim 60 , wherein the biological sample type is selected from the group consisting of liver cells, epithelial cells, endothelial cells, kidney cells, prostate cells, blood cells, lung cells, brain cells, skin cells, adipose cells, tumor cells, and mammary cells.  
     
     
         70 . The method of  claim 60 , wherein the plurality of data sets is derived from one biological sample type.  
     
     
         71 . The method of  claim 60 , wherein the plurality of data sets is derived from one biological sample type that is treated differently.  
     
     
         72 . The method of  claim 60 , wherein the plurality of data sets are derived from biological samples taken at different times for the same organism.  
     
     
         73 . The method of  claim 60 , wherein the biological system is in a mammal.  
     
     
         74 . An article of manufacture having a computer-readable medium with computer-readable instructions embodied thereon for performing the method of  claim 60 .  
     
     
         75 . A method of profiling a state of an animal, the method comprising the steps of: 
 (a) providing a plurality of data sets comprising different types of measurements of a gene transcript, a protein, or a metabolite derived from a sample of an animal;    (b) preprocessing the plurality of the data sets to generate preprocessed data sets;    (c) evaluating the preprocessed data sets with a multivariate analysis and correlating features among the preprocessed data sets to determine one or more sets of differences among at least a portion of the plurality of data sets;    (d) generating a profile of one or more biomarkers in response to one or more correlations, the profile characterizing a state of the animal; and    (e) displaying at least a portion of the data relevant to the profile.    
     
     
         76 . A method of profiling a state of an animal, the method comprising the steps of: 
 (a) analyzing a sample of an animal to provide a plurality of data sets, the plurality of data sets comprising different types of measurements of a gene transcript, a protein, or a metabolite;    (b) preprocessing the plurality of data sets to generate preprocessed data sets;    (c) evaluating the preprocessed data sets with a multivariate analysis and correlating features among the plurality of the data sets to determine one or more sets of differences among at least a portion of the plurality of data sets; and    (d) generating a profile of one or more biomarkers in response to one or more correlations, the profile characterizing a state of the animal.