Methods of determining protein activity levels using gene expression profiles

A method of identifying a cell of a cell type, that has one or more genetic mutations or polymorphisms that disrupt activity of a corresponding gene product, comprising determining a level of perturbation to said gene product at which the similarity is greatest between a diagnostic profile and a perturbation response profile extracted from perturbation response curves for said determined level of perturbation to said gene product, said diagnostic profile having been obtained by a method comprising measuring a first plurality of cellular constituents in said cell, wherein said perturbation response curves are the products of a method comprising

• (i) providing perturbation response profiles of said gene product for said cell type, wherein said perturbation response profiles are obtained by measuring a second plurality of cellular constituents in a wild type cell of said cell type at a plurality of discrete levels of perturbation to said gene product, and
• (ii) interpolating said perturbation response profiles so that a perturbation response profile may be extracted over a range of levels of perturbation to said gene product, wherein said interpolated response profiles comprise said perturbation response curves,
• wherein said determined level of perturbation to said gene product represents the extent to which the activity of said gene product is disrupted, and wherein cells in which the determined gene product activity is disrupted are identified as having said genetic mutations or polymorphisms.

A method for measuring activity of a drug in vivo comprising determining an activity level of a protein in a cell treated with said drug according to a method comprising determining a level of perturbation to said protein at which similarity is greatest between a diagnostic profile and a perturbation response profile extracted from perturbation response curves for the determined level of perturbation to said protein, wherein:

• (a) the diagnostic profile is obtained by a method comprising measuring a first plurality of cellular constituents in the cell treated with said drug;
• and
• (b) the perturbation response curves are provided by a method comprising
• (i) providing perturbation response profiles of said protein for a cell, wherein said perturbation response profiles are obtained by a method comprising measuring a second plurality of cellular constituents in a cell at a plurality of discrete levels of perturbation to said protein,
• (ii) interpolating said perturbation response profiles so that a perturbation response profile may be extracted over a range of levels of perturbation to said protein, wherein said interpolated response profiles comprise said perturbation response curves,
• and wherein said determined level of perturbation to said protein represents said protein activity level in said cell treated with said drug and said protein activity level is a measure of said drug activity.

A method of determining the dose of one or more drugs to achieve a desired clinical effect in a patient comprising determining a dose of said one or more drugs where similarity is greatest between a diagnostic profile and a perturbation response profile associated with the desired clinical effect, wherein

• (a) the diagnostic profile is provided by a method comprising measuring a first plurality of cellular constituents in one or more cells from said patient treated with said one or more drugs;
• and
• (b) the perturbation response profile associated with the desired clinical effect is provided by a method comprising
• (i) providing a plurality of perturbation response profiles of said one or more drugs for one or more cells of one or more patients, wherein said plurality of perturbation response profiles is obtained by a method comprising measuring a second plurality of cellular constituents in one or more cells at a plurality of discrete levels of exposure to said one or more drugs, and
• (ii) calibrating said plurality of perturbation response profiles to clinical effects of the one or more drugs.

A method for determining a drug therapy to achieve a desired clinical effect in a patient comprising determining a drug therapy where similarity is greatest between a diagnostic profile and a perturbation response profile associated with the desired clinical effect, wherein

• (a) the diagnostic profile is provided by a method comprising measuring a first plurality of cellular constituents in one or more cells from said patient treated with said drug therapy;
• and
• (b) the perturbation response profile associated with the desired clinical effect is provided by a method comprising
• (i) providing a plurality of perturbation response profiles for a plurality of drug therapies, wherein said plurality of perturbation response profiles is obtained by a method comprising measuring a second plurality of cellular constituents in one or more cells for a plurality of drug therapies, and
• (ii) calibrating said plurality of perturbation response profiles to clinical effects of the plurality of drug therapies.

A kit for determining the level of activity of a protein in a cell type, said kit comprising:

• (a) a solid phase containing on its surface a plurality of nucleic acids of different sequences, each at a known location on said solid phase, each nucleic acid capable of hybridizing to an RNA species or cDNA species derived therefrom, said RNA species known to be increased or decreased in response to a perturbation to said protein in said cell type;
• and
• (b) computer readable medium having perturbation response curves encoded thereon, wherein said perturbation response curves are the product of a method comprising:
• (i) providing perturbation response profiles of said protein for said cell type, wherein said perturbation response profiles are obtained by measuring a second plurality of cellular constituents in a cell of said cell type at a plurality of discrete levels of perturbation to said protein;
• and
• (ii) interpolating said perturbation response profiles so that a perturbation response profile may be extracted over a continuous range of levels of perturbation to said protein
• wherein said interpolating response profiles comprise said perturbation response curves.

A method of identifying a cell of a cell type, that has one or more genetic mutations or polymorphisms that disrupt activity of one or more corresponding gene products, comprising determining a level of perturbation to each said gene product at which the similarity is greatest between a diagnostic profile and a combination of perturbation response profiles extracted from perturbation response curves for each said gene product for each said determined level of perturbation, said diagnostic profile having been obtained by a method comprising measuring a first plurality of cellular constituents in said cell, wherein said perturbation response curves for each said gene products are the products of a method comprising

• (i) providing perturbation response profiles of said gene product for said cell type, wherein said perturbation response profiles are obtained by measuring a second plurality of cellular constituents in a wild type cell of said cell type at a plurality of discrete levels of perturbation to said gene product, and
• (ii) interpolating said perturbation response profiles so that a perturbation response profile may be extracted over a range of levels of perturbation to said gene product, wherein said interpolated response profiles comprise said perturbation response curves,
• wherein said determined level of perturbation to each said gene product represents the extent to which the activity of said gene product is disrupted, and wherein cells in which corresponding gene product activities are disrupted are identified as having genetic mutations or polymorphisms in said genes.

A method for determining a level of activity of a biologically active cellular constituent of interest, said method comprising determining a level of perturbation to the cellular constituent of interest at which similarity is greatest between a diagnostic profile and a perturbation response profile extracted from perturbation response curves for said determined level of perturbation to the cellular constituent of interest,

• said diagnostic profile having been obtained by a method comprising measuring a first plurality of cellular constituents in a cell of said cell type,
• said perturbation response curves being the products of a method comprising:
• (i) providing perturbation response profiles of the cellular constituent of interest for said cell type, wherein said perturbation response profiles are obtained by measuring a second plurality of cellular constituents in a cell of said cell type at a plurality of discrete levels of perturbation to the cellular constituent of interest, and
• (ii) interpolating said perturbation response profiles so that a perturbation response profile may be extracted over a range of levels of perturbation to the cellular constituent of interest, wherein said interpolated response profiles comprise said perturbation response curves,
• wherein said determined level of perturbation to the cellular constituent of interest represents the activity level of said cellular constituent of interest in said cell type.

A method for determining a level of activity of a protein in a cell type, said method comprising:

• (a) obtaining a diagnostic profile by a method which comprises measuring a first plurality of cellular constituents in a cell of said cell type;
• and
• (b) determining a level of perturbation to said protein at which similarity is greatest between said diagnostic profile and a perturbation response profile extracted from perturbation response curves for said determined level of perturbation to said protein, said perturbation response curves being products of a method comprising:
• (i) providing perturbation response profiles of said protein for said cell type, wherein said perturbation response profiles are obtained by measuring a second plurality of cellular constituents in a cell of said cell type at a plurality of discrete levels of perturbation to said protein, and
• (ii) interpolating said perturbation response profiles so that a perturbation response profile may be extracted over a range of levels of perturbation to said protein, wherein said interpolated response profiles comprise said perturbation response curves,
• wherein said determined level of perturbation to said protein represents said protein activity level in said cell type.