Abstract: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Abstract: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: A method is provided for identifying complexes between a transcription factor and another protein, such as another different transcription factor. The method includes the steps of isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes include a particular type of transcription factor; and identifying which of the multiple different proteins are present in the isolated transcription factor complexes.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: Methods, compositions and kits are provided for sensitive and quantitative detection of nucleic acid, especially for the determination of the presence and/or amount of a target nucleic acid with mutations or single nucleotide polymorphism (SNP). In particular, assays are provided for amplifying a target nucleic acid via ligation of designed oligonucleotide probes and linear amplification by using an RNA polymerase, such as T7 polymerase. The assays can be used for diagnosis, prognosis or monitoring of diseases or disorders, for pharmacogenomic studies of patient stratification and drug responses, for discovery of therapeutic targets, or for forensic analysis.

Abstract: Methods, compositions and kits are provided for high throughput detection of micro RNAs (miRNA), especially for sensitive and specific detection of miRNA that are in low abundance and closely related to each other. In particular, an assembly of designed oligonucleotide probes with unique tag sequences is used to achieve these purposes via high throughput microarrays, optionally in conjunction with branched-DNA based array detection. The assays can be used for diagnosis, prognosis or monitoring of diseases or disorders such as cancer, for pharmacogenomic studies of patient stratification and drug responses, for discovery of therapeutic targets, or for forensic analysis.

Abstract: Rapid, sensitive, reproducible high-throughput methods for detecting methylation patterns in samples of nucleic acid, especially in the promoter region of genes which are enriched with CpG islands, are provided. The methods include isolating complexes of methylated DNA and methylation binding protein, optionally amplifying the isolated methylated DNA, and detecting the methylated DNA or its amplification products in a multiplex and robust manner. By using the inventive methodology, methylated and unmethylated sequences present in the original sample of nucleic acid can be distinguished. By profiling and comparing the methylation status of genes in different samples, one can utilize the information for diagnosis and treatment of diseases or conditions associated with aberrant DNA hypermethylation or hypomethylation.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less with several embodiments having half lives of 4 hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Abstract: Methods, arrays and kits are provided for rapidly and efficiently identifying and quantifying multiple different activated transcription factors in a biological sample at the same time. In one aspect, a method is provided for isolating DNA probes which bind to activated transcription factors, including the step of mixing a library of double stranded DNA probes with a sample containing activated transcription factors. The transcription factor probes that have bound to the activated transcription factors are isolated from the mixture via an agarose gel separation. The bound probes can be identified, for example, by using an array of hybridization probes.

Abstract: Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less with several embodiments having half lives of 4 hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Abstract: The present invention provides methods, compositions and kits for highly efficient, high throughput detection of mutation or nucleotide variation of an organism. By exploiting the molecular interactions between strands of nucleic acid and between nucleic acid and protein, assays have been developed to detect nucleotide variation, in particular, single nucleotide polymorphism (SNP) in various biological samples including human genomic DNA and virus. In preferred embodiments, immunoassays are developed to specifically capture a nucleic acid-protein complex formed between a 4-way nucleic acid structure called Holliday junction and a protein that specifically recognizes the Holliday junction. These assays can be used in a wide variety of applications such as diagnostics, genotyping, genetic profiling, mutation detection, disease prevention, therapeutic treatment, and screening for therapeutic targets or therapeutics.

Abstract: Method and kits are provided for screening for transcription factor modulators efficiently. In one aspect, the method can be employed to profile multiple, different transcription factors activated in a sample in the presence of each of the transcription factor modulators. Comparison of the activated transcription factor profiles in the presence and absence of the modulator identifies the transcription factor modulator that modulates the activation of specific transcription factors.

Abstract: Methods, arrays and kits are provided for rapidly and efficiently identifying the cell type of a cell sample. In one embodiment, the method includes the step of mixing a library of double-stranded DNA probes with a cell sample containing activated transcription factors. The DNA probes that have bound to the activated transcription factors may be isolated from the complexes formed between the probes and the activated transcription factors. The bound probes can be identified, for example, by using an array of hybridization probes, which leads to the determination of the cell type of the cell sample based on the correlation between the identified DNA probes and their corresponding transcription factors.