Abstract: A method of determining water quality of a water sample, comprising exposing the water sample to a test cell system; generating at least one profile of ensuing changes in activities of transcription factors in the test cell system in response to such exposing; and determining from the generated at least one profile the water quality of the water sample. Computer systems and kits for carrying out the water quality determination of water specimens are also described, in which water quality can be readily and accurately determined by transcription factor activity analysis.

Abstract: Methodology is described for identification of perturbagens of biological processes and cell systems through transcription factor activity profiling. The method is based on the unexpected finding that perturbagens of a particular biological process or a cell system within living cells produce an invariant transcription factor activity profile (TFAP), regardless of where and how said perturbagens interfere. Such invariant TFAPs have been identified for perturbagens of multiple biological processes and cell systems, including mitochondria, HDAC, and proteasome inhibitors; DNA damaging agents; cytoskeleton disruptors; and kinase inhibitors. The discovery of such invariant TFAP signatures opens a vast spectrum of applications, including drug discovery and repurposing of approved drugs, and provides a new ontological basis for characterization of biological properties of myriad chemical and biological compounds.

Abstract: A protein reporter system comprising at least one reporter including a response element responsive to the binding of a transcription factor, a secreted enzyme backbone and a recognition region for specific binding of an antibody. Multiplexed assays for binding, assaying and quantifying the activity of transcription factors are also described, in which the assays use protein reporters in sets, libraries or other groupings, as necessary to achieve desired quantification.

Abstract: A protein reporter system comprising at least one reporter including a response element responsive to the binding of a transcription factor, a secreted enzyme backbone and a recognition region for specific binding of an antibody. Multiplexed assays for binding, assaying and quantifying the activity of transcription factors are also described, in which the assays use protein reporters in sets, libraries or other groupings, as necessary to achieve desired quantification.

Abstract: A method of determining biosimilarity of a sample composition to a reference composition, including: exposing a test cell system to a sample composition so that the test cell system responds to the sample composition by change in transcription factor activity in the test cell system; generating from the test cell system response an output correlative to the change of transcription factor activity in the test cell system; and determining from comparison of said output with a transcription factor activity reference standard for the reference composition, the biosimilarity of the sample composition to the reference composition. Computer systems and kits for carrying out the determination of biosimilarity of compositions are also described, in which biosimilarity of compositions ranging from simple molecules to complex mixtures can be readily and accurately determined by transcription factor activity analysis.

Abstract: A method of determining water quality of a water sample, comprising exposing the water sample to a test cell system; generating at least one profile of ensuing changes in activities of transcription factors in said test cell system in response to said exposing; and determining from the generated at least one profile the water quality of the water sample. Computer systems and kits for carrying out the water quality determination of water specimens are also described, in which water quality can be readily and accurately determined by transcription factor activity analysis.

Abstract: Compositions, methods and kits are provided that are useful, for example, for determining activities of multiple cis-regulatory sequences, such as promoters and enhancers, and/or multiple trans-acting factors, such as transcription factors, in a cell. In particular, in certain embodiments, compositions are provided comprising a population of polynucleotide reporter transcription units (RTUs) in which each RTU comprises a reporter sequence, a processing tag located in the reporter sequence; and a cis-regulatory element operably linked to the reporter sequence, wherein the reporter sequences between any two RTUs in the population, outside of the processing tags, are substantially identical and wherein the positions of the processing tags within the reporter sequences distinguish between any two RTUs differing, for example, in their cis-regulatory elements. The compositions, methods and kits can further be used, for example, to identify a cell type or disease state, for example, in a biological organism.