Abstract: The present invention includes methods and apparatus for use in rapid testing for and prediction of a PPAR? response (i.e. a response similar to that of PPAR? agonists). The invention includes a PPAR? response signature comprising a set of twenty genes. The invention discloses methods whereby the differential expression of the genes of the PPAR? response signature may be used to predict whether a compound will induce a PPAR? response in a test subject.

Abstract: The invention discloses reagent sets and gene signatures for predicting onset of renal tubule injury in a subject. The invention also provides a necessary set of 186 genes useful for generating signatures of varying size and performance capable of predicting onset of renal tubule injury. The invention also provides methods, apparatuses and reagents useful for predicting future renal tubule injury based on expression levels of genes in the signatures. In one particular embodiment the invention provides a method for predict whether a compound will induce renal tubule injury using gene expression data from sub-acute treatments.

Abstract: Disclosed is a method for predicting the biological activity of a compound by the similarity of its drug signature score to the scores of a plurality of known drug signatures.

Abstract: The present invention discloses methods of data analysis directed to diagnostic development, and in particular the development of signatures for classifying chemogenomic data. The invention provides methods for identifying and functionally characterizing a “necessary” set of information rich variables. The invention also discloses methods for identifying a plurality of “sufficient” classifiers. The necessary set of variables may be incorporated into a single diagnostic device to provide simultaneous confirmation of a classification measurement with a plurality of independent classifiers. In the field of biological diagnostics, the invention may be used to provide a plurality of short lists of genes, referred to as “signatures” that are “sufficient” to carry out specific classification tasks such as predicting the activity and side effects of a compound in vivo.

Abstract: The present invention provides methods and compositions for use in rapid test or prediction of the propensity of a test compound to induce cholesterol reduction in a subject. The invention also includes a cholesterol reduction signature as well as the method of deriving such signature.

Abstract: The present invention provides methods and compositions for use in rapid test or prediction of the propensity of a test compound to induce cholestasis in a subject. The invention also includes a Cholestasis signature database as well as the method of deriving such database.

Abstract: The invention provides systems and methods for remote computer-based analysis of user provided chemogenomic data. The invention includes computer-based systems and software that allow a remote user to access a centralized comprehensive chemogenomic database and use the correlative tools of that database to assess the user's data. The tools allow the user to generate a summary report of the chemogenomic/toxicogenomic analysis results obtained using the chemogenomic database.

Abstract: Apparatus and method for classifying multi-dimensional biological data are described. In some embodiments, a methodology for deriving a linear classification rule can be used for predicting a biological activity or a biological state. Advantageously, the methodology described herein facilitates obtaining robust and sparse classifiers that account for uncertainty involved in real-world experiments and improve computational efficiency and ease of interpretation of results.

Abstract: The invention provides methods for preparing reagent sets based on small subsets of highly informative genes capable of carrying out a broad range of chemogenomic classification tasks. The invention also provides high-throughput diagnostic assays and devices based on these reduced subsets of information rich genes. In addition, the invention provides a general method for selecting a reduced subset of highly responsive variables from a much larger multivariate dataset, and thus, use of these variables to prepare diagnostic measurement devices, or other analytic tools, with little or no loss of performance relative to devices or tools incorporating the full set of variables.

Abstract: The invention discloses reagent sets and gene signatures for predicting onset of renal tubule injury in a subject. The invention also provides a necessary set of 186 genes useful for generating signatures of varying size and performance capable of predicting onset of renal tubule injury. The invention also provides methods, apparatuses and reagents useful for predicting future renal tubule injury based on expression levels of genes in the signatures. In one particular embodiment the invention provides a method for predict whether a compound will induce renal tubule injury using gene expression data from sub-acute treatments.

Abstract: The invention discloses reagent sets and gene signatures for predicting onset of renal tubule injury in a subject. The invention also provides a necessary set of 186 genes useful for generating signatures of varying size and performance capable of predicting onset of renal tubule injury. The invention also provides methods, apparatuses and reagents useful for predicting future renal tubule injury based on expression levels of genes in the signatures. In one particular embodiment the invention provides a method for predict whether a compound will induce renal tubule injury using gene expression data from sub-acute treatments.

Abstract: The present invention discloses methods of data analysis directed to diagnostic development, and in particular the development of signatures for classifying chemogenomic data. The invention provides methods for identifying and functionally characterizing a “necessary” set of information rich variables. The invention also discloses methods for identifying a plurality of “sufficient” classifiers. The necessary set of variables may be incorporated into a single diagnostic device to provide simultaneous confirmation of a classification measurement with a plurality of independent classifiers. In the field of biological diagnostics, the invention may be used to provide a plurality of short lists of genes, referred to as “signatures” that are “sufficient” to carry out specific classification tasks such as predicting the activity and side effects of a compound in vivo.

Abstract: The present invention provides methods and compositions for producing high titer preparations of recombinant AAV (“rAAV”) virions. The compositions of the present invention include AAV helper function systems and host cells. The present invention also includes methods of using AAV helper function vectors that effect the production of only small amounts of the long forms of Rep protein, and rAAV virions produced by such methods.

Abstract: Disclosed is a method for predicting the propensity of a compound to cause depletion of reticulocytes in a mammal.

Abstract: The present invention provides methods and compositions for producing high titer preparations of recombinant AAV (“rAAV”) virions. The compositions of the present invention include AAV helper function systems and host cells. The present invention also includes methods of using AAV helper function vectors that effect the production of only small amounts of the long forms of Rep protein, and rAAV virions produced by such methods.

Abstract: Methods for deriving and using Group Signatures and Drug Signatures are provided, wherein Group Signatures comprise a plurality of genes, modulated expression of which is characteristic and specific of a group of related drug compounds, and wherein Drug Signatures comprise a plurality of genes, modulated expression of which is characteristic and specific for individual drug compounds.

Abstract: The present invention provides methods and compositions for producing high titer preparations of recombinant AAV (“rAAV”) virions. The compositions of the present invention include AAV helper function systems and host cells. The present invention also includes methods of using AAV helper function vectors that effect the production of only small amounts of the long forms of Rep protein, and rAAV virions produced by such methods.

Abstract: The present invention provides methods and compositions for producing high titer preparations of recombinant AAV (“rAAV”) virions. The compositions of the present invention include AAV helper function systems and host cells. The present invention also includes methods of using AAV helper function vectors that effect the production of only small amounts of the long forms of Rep protein, and rAAV virions produced by such methods.

Abstract: A two-step, scalable method is described for identifying the cellular function(s) of one or more genes of unknown function, and for identifying modulators of the gene(s). The method uses the reversal or alteration of a phenotype created by the expression of the heterologous gene, e.g., a human gene, to identify modulators of that gene's activity. That modulator is then used in an in vitro or in vivo disease model system to identify compounds which affect disease progression. The subset of compounds which influence disease in a therapeutic manner are drug leads. However, all compounds which influence disease progression are tools to at least partially characterize gene function. The inhibitor identification step of the method is preferably carried out using a plurality of microbial strains or cell lines expressing different heterologous DNA sequences in a single solution. The method is particularly useful for genes which have not been validated as good inhibitor targets.

Abstract: Methods of screening for antimicrobial agents or other compounds active on a particular strain are described. These methods use pools of strains of cells or microbes in order to screen for activity on many cellular targets in a single screen. The strain or strains in the pool for which growth is inhibited or stimulated are determined; such identification can also provide a means of identifying the cellular target on which a compound is active.