Methods and systems for profiling biological systems

1 . A method of profiling a state of a biological system in a mammal, the method comprising the steps of:

(a) evaluating with statistical analysis a plurality of data sets of a biological system and comparing features among the plurality of data sets to determine one or more sets of differences among at least a portion of the plurality of data sets; and

(b) developing a profile for a state of the biological system based on the results of step (a),

wherein the plurality of data sets comprise measurements derived from more than one biological sample type, more than one type of measurement technique, more than one biomolecular component type, or a combination of at least two of a biological sample type, a measurement technique, and a biomolecular component type.

2 . The method of claim 1 wherein the biological system is in a human.

3 . The method of claim 1 wherein the statistical analysis comprises multivariate analysis.

4 . The method of claim 1 wherein the biological sample type is selected from the group comprising blood, plasma, serum, cerebrospinal fluid, bile, saliva, synovial fluid, pleural fluid, pericardial fluid, peritoneal fluid, sweat, feces, nasal fluid, ocular fluid, intracellular fluid, intercellular fluid, lymph, urine, 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.

5 . The method of claim 1 wherein a plurality of data sets are derived from one biological sample type that is treated differently, or from one biological sample type that is collected or analyzed at different times.

6 . The method of claim 1 wherein the measurement technique is selected from the group comprising liquid chromatography, gas chromatography, high performance liquid chromatography, capillary electrophoresis, mass spectrometry, liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, high performance liquid chromatography-mass spectrometry, capillary electrophoresis-mass spectrometry, nuclear magnetic resonance spectrometry, parallel hybridization assay, parallel sandwich assay, and competitive assay.

7 . The method of claim 1 wherein a plurality of data sets comprise measurements from different instrument configurations of a single type of measurement technique.

8 . The method of claim 1 wherein the biomolecular component type is a gene, a gene transcript, a protein, or a metabolite.

9 . The method of claim 1 comprising the step of comparing the profile for a state of the biological system to a database of profiles.

10 . The method of claim 1 comprising comparing the profile for a state of the biological system to a profile of another state of a biological system.

11 . An article of manufacture having a computer-readable medium with computer-readable instructions embodied thereon for performing the method of claim 1 .

12 . A method of profiling a state of a biological system in a mammal, the method comprising the steps of:

(a) evaluating with statistical analysis a plurality of data sets for a biomolecular component type and comparing features among the plurality of data sets to determine one or more sets of differences among at least a portion of the plurality of data sets;

(b) evaluating with statistical analysis a plurality of data sets for another biomolecular component type and comparing features among the plurality of data sets to determine one or more sets of differences among at least a portion of the plurality of data sets; and

(c) correlating the results of step (a) and step (b) to develop a profile for a state of the biological system.

13 . The method of claim 12 wherein the plurality of data sets for a biomolecular component type or another biomolecular component type comprise measurements derived from more than one biological sample type, more than one type of measurement technique, or a combination of a biological sample type and a measurement technique.

14 . The method of claim 12 wherein the biomolecular component type is a protein and the other biomolecular component type is a metabolite.

15 . The method of claim 12 wherein the biomolecular component type is a gene transcript and the other biomolecular component type is a metabolite.

16 . A method of profiling a state of a biological system in a mammal, the method comprising the steps of:

(a) evaluating with statistical analysis a plurality of data sets comprising measurements from at least two biomolecular component types and comparing features among the plurality of data sets to determine one or more sets of differences among at least a portion of the plurality of data sets; and

(b) developing a profile for a state of the biological system based on the results of step (a).

17 . The method of claim 16 wherein the plurality of data sets comprise measurements derived from more than one biological sample type, more than one type of measurement technique, or a combination of a biological sample type and a measurement technique.

18 . The method of claim 16 wherein the step of evaluating comprises:

evaluating a plurality of data sets for a biomolecular component type and comparing features among the plurality of data sets to determine one or more sets of differences among at least a portion of the plurality of data sets; and

evaluating a plurality of data sets for another biomolecular component type and comparing features among the plurality of data sets to determine one or more sets of differences among at least a portion of the plurality of data sets.

19 . The method of claim 16 wherein the at least two biomolecular component types comprise a protein and a metabolite.

20 . The method of claim 16 wherein the at least two biomolecular component types comprise a gene transcript and a metabolite.