306 results about "Expression pattern" patented technology

This invention relates to an array, including a universal micro-array, for the analysis of nucleic acids, such as DNA. The devices and methods of the invention can be used for identifying gene expression patterns in any organism. More specifically, all possible oligonucleotides (n-mers) necessary for the identification of gene expression patterns are synthesized. According to the invention, n is large enough to give the specificity to uniquely identify the expression pattern of each gene in an organism of interest, and is small enough that the method and device can be easily and efficiently practiced and made. The invention provides a method of analyzing molecules, such as polynucleotides (e.g., DNA), by measuring the signal of an optically-detectable (e.g., fluorescent, ultraviolet, radioactive or color change) reporter associated with the molecules. In a polynucleotide analysis device according to the invention, levels of gene expression are correlated to a signal from an optically-detectable (e.g. fluorescent) reporter associated with a hybridized polynucleotide. The invention includes an algorithm and method to interpret data derived from a micro-array or other device, including techniques to decode or deconvolve potentially ambiguous signals into unambiguous or reliable gene expression data.

Described herein are therapeutic targets expressed in cancer stem cells and methods for treating and diagnosing cancer by targeting such cells with antibodies, compounds, nucleic acid, or other therapeutic agent. In one embodiment described herein, therapeutic agents for the treatment of cancer are provided based on the identification of cancer stem cell targets. The present invention also includes therapeutic targets for cancer therapy and cancer stem cell-targeted therapy. The invention includes the treatment of cancer by the administration of compounds or agents that target cancer stem cells.

To gain a better understanding of brain tumor angiogenesis, new techniques for isolating brain endothelial cells (ECs) and evaluating gene expression patterns were developed. When transcripts from brain ECs derived from normal and malignant colorectal tissues were compared with transcripts from non-endothelial cells, genes predominantly expressed in the endothelium were identified. Comparison between normal- and tumor-derived endothelium revealed genes that were specifically elevated in tumor-associated brain endothelium. These results confirm that neoplastic and normal endothelium in human brains are distinct at the molecular level, and have significant implications for the development of anti-angiogenic therapies in the future.

Methods, systems, and apparatuses for detecting and describing heterogeneity in a cell sample are disclosed herein. A plurality of fields of view (FOV) are generated for one or more areas of interest (AOI) within an image of the cell sample are generated. Hyperspectral or multispectral data from each FOV is organized into an image stack containing one or more z-layers, with each z-layer containing intensity data for a single marker at each pixel in the FOV. A cluster analysis is applied to the image stacks, wherein the clustering algorithm groups pixels having a similar ratio of detectable marker intensity across layers of the z-axis, thereby generating a plurality of clusters having similar expression patterns.

A method for screening for a trait associated with the altered expression of a gene of interest in plants is provided. The method is a combinatorial approach which uses traditional plant breeding techniques for modifying the patterns of expression of a gene of interest. Kits for use in the method and transgenic plants generated by the method are also provided.

The present invention provides a process for classification of cancers and tissues of origin through the analysis of the expression patterns of specific microRNAs and nucleic acid molecules relating thereto. Classification according to a microRNA tree-based expression framework allows optimization of treatment, and determination of specific therapy.

Biomarkers having expression patterns that correlate with a response of cells to treatment with one or more cdk modulating agents, and uses thereof. Also provided are methods for testing or predicting whether a mammal will respond therapeutically to a method of treating cancer that comprises administering an agent that modulates cdk activity.

Provided are methods of diagnosis, prognosis, and monitoring of aging using biomarkers that have been discovered to be linked to biological aging process. Methods for increasing neural cell regeneration and cognitive function are also provided. The methods are, at least in part, based on a discovery that altered expression patterns of certain biological markers are associated with biological aging processes. These markers comprise at least Eotaxin/CCL11, 2-microglobulin, MCP-1 and Hap-toglobulin, increased expression of which has been shown to be associated with increase in biological aging process.

A terminal device, which is to be connected to the network together with other terminal devices and a host device to operate the terminal device, includes an output device that outputs perceptually recognized information, a self-pattern storing system that stores information on an expression pattern for the terminal device, a configuring system that configures the information into the self-pattern storing system, an output executing system that makes the output device output the expression pattern, based upon the written information, an obtaining system that obtains information on expression patterns for the other terminal devices, and a setting system that defines an expression pattern different from any of the expression patterns for the other terminal devices as the expression pattern for the terminal device, based upon the obtained information, and sets information on the defined expression pattern as the information to be written.

Methods are provided for classification of cancers by the expression of a set of genes referred to as the core serum response (CSR), or a subset thereof. The expression pattern of the CSR in normal tissues correlates with that seen in quiescent fibroblasts cultured in the absence of serum, while cancer tissues can be classified as having a quiescent or induced CSR signature. Patients with the induced CSR signature have a higher probability of metastasis. Classification according to CSR signature allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like.

A system, methods, and apparatus are described to collect and prepare single cells and groups of cells from microsamples of specimens and encode spatial information of the physical position of the cells in the specimen. In some embodiment, beads or surfaces with oligonucleotides containing spatial barcodes are used to analyze DNA or RNA. The spatial barcodes allow the position of the cell to be defined and the nucleic acid sequencing information, such as target sequencing, whole genome, gene expression, used to analyze the cells in a microsample for cell type, expression pattern, DNA sequence, and other information, in the context of the cell's physical position in the specimen. In other embodiment, markers such as isotopes are added to a microsample to encode spatial position with mass spectoscopy or other analysis. The spatial encoded information is then readout by analysis such as DNA sequencing, mass spectrometry, fluorescence, or other methods.

The present invention provides methods for diagnosing neurodegenerative disease, such as Alzheimer's Disease, Parkinson's Disease, and dementia with Lewy body disease by detecting a pattern of gene product expression in a cerebrospinal fluid sample and comparing the pattern of gene product expression from the sample to a library of gene product expression pattern known to be indicative of the presence or absence of a neurodegenerative disease. The methods also provide for monitoring neurodegenerative disease progression and assessing the effects of therapeutic treatment. Also provided are kits, systems and devices for practicing the subject methods.

The present invention provides systems and methods for analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, including comparative differential expression analysis, expression pattern matching, and mapping of external attributes or identifiers to internal representations of gene fragments or samples.