49 results about "Gene interaction" patented technology

The present invention provides methods and systems or apparatuses, to analyze multiple molecular and clinical variables from an individual diagnosed with a psychiatric disorder, such as post-traumatic stress disorder (PTSD), in order to optimize medication selection for therapeutic response. Molecular co-variables include polymorphisms in genes including those involved in central control and mediation of the hypothalamic-pituitary axis (HPA) stress response, the density of methylation in regulatory regions of said polymorphic genes, polymorphisms in genes that encode cytochrome P450 enzymes responsible for drug metabolism, and drug-drug and drug-gene interactions. Clinical co-variables include but are not limited to the sex, age and ethnicity of that individual, medication history, family history, diagnostic codes, Pittsburgh insomnia rating score, and Charlson index score. The system makes a determination based on unstructured and structured data types derived from internal and external knowledge resources to determine psychotropic drug choice that best matches the molecular and clinical variation profile of an individual patient. The decision support system provides a therapeutic recommendation for a clinician based on the patient's variation profile.

The present invention provides protein fragment complementation assays for drug discovery, in particular to identify compounds that activate or inhibit cellular pathways. Based on the selection of an interacting protein pair combined with an appropriate PCA reporter, the assays may be run in high-throughput or high-content mode and may be used in automated screening of libraries of compounds. The interacting pair may be selected by cDNA library screening; by gene-by-gene interaction mapping; or by prior knowledge of a pathway. Fluorescent and luminescent assays can be constructed using the methods provided herein. The selection of suitable PCA reporters for high-throughput or high-content (high-context) assay formats is described for a diversity of reporters, with particular detail provided for examples of monomeric enzymes and fluorescent proteins. Methods are described for constructing such assays for one or more steps in a biochemical pathway; testing the effects of compounds from combinatorial, natural product, peptide, antibody, nucleic acid or other diverse libraries on the protein or pathway(s) of interest; and using the results of the screening to identify specific compounds that activate or inhibit the protein or pathway(s) of interest. Single-color and multi-color assays are disclosed. Further disclosed are universal expression vectors with cassettes that allow the rapid construction of assays for a large and diverse number of gene / reporter combinations. The development of such assays is shown to be straightforward, providing for a broad, flexible and biologically relevant platform for drug discovery.

The invention provides a cloning and transient expression method of persimmon deastringency related genes. The method comprises: first acquiring gene 3'-terminal sequences, then employing 3' RACE (rapid amplication of cDNA ends) technology to acquire 3'-terminal sequences of ADH and PDC gene family members in persimmon fruits; adopting Q-PCR (quantitative polymerase chain reaction) technology to analyze the genetic expression of ADH and PDC gene family members in a persimmon fruit deastringency treatment; and conducting separation to obtain full-length sequences of ADH and PDC gene family members, then establishing a transient expression system of persimmon leaves. The method of the invention clones the persimmon deastringency related gene family members, analyze the expression patterns of the family members in the persimmon deastringency treatment, and finally verifies functions of the target genes through transient expression of the persimmon leaves. The invention clarifies the regulation mechanism for postharvest persimmon deastringency from the molecular mechanism aspective, and can be used for further functional verification (transgenosis, gene interaction and the like) study of the postharvest persimmon deastringency mechanism.

A method of introducing a molecule of interest into a plant cell having a cell wall includes interacting a gamma-zein peptide with a molecule of interest to form a gamma-zein linked structure. The gamma-zein linked structure is then placed in contact with the plant cell having a cell wall, and allowing uptake of the gamma-zein linked structure into the plant cell. Alternatively, a gene of interest can be expressed in a plant cell having an intact cell wall by interacting a gamma-zein peptide with the gene of interest to form a gamma-zein linked gene structure, allowing uptake of the gamma-zein linked gene structure into the plant cell, and expressing the gene of interest in the plant cell and its progeny.

The present invention provides a method for identifying plant lncRNA and gene interaction, and relates to the technical field of molecular genetics. The method comprises the following steps: population SNP genotype data of lncRNA and gene are obtained; population expression data of the gene in a studied tissue are obtained; target trait population phenotypic data are obtained; the population SNP genotype data and target trait population phenotypic data are subjected to correlation analysis; the population SNP genotype data and population expression data are subjected to correlation analysis; acorrelation coefficient r of the population SNP genotype data and target trait population phenotypic data is calculated; when three limit conditions are met at the same time, the lncRNA interacts with the gene to commonly affect phenotypic variation of plant target traits. The method is used to accurately detect interaction between populus tomentosa lncRNA LNC-0052611 and gene Pto-COMT25, and theinteraction affects the phenotypic variation of diameter at breast height of populus tomentosa.

The invention discloses a gene-gene interaction recognition method based on the sparsity factor analysis (Sparse Factor Analysis for Epistasis, EPISFA). The method comprises the following steps of 1)entering genotype raw data and screening according to a linkage disequilibrium coefficient between genes; 2) randomly dividing the data into blocks; 3) dividing the data into diseased and non-diseasedgroups according to a disease state, calculating the correlation coefficient matrix of two groups, and using Fisher transform to deduct gene site correlation of the correlation coefficient matrix ofthe two groups; 4) learning model weights using a sparsity factor analysis method; 5) conducting cross-validation, selecting model parameters, and identifying corresponding gene-gene interaction. Experiments show that the statistical efficiency and computational efficiency of the method are both high and the method has good application prospects.

The invention relates to data mining in bioinformatics, and particularly to a method for identifying the cancer-related miRNA through a miRNA-gene regulation module. The method comprises the steps ofperforming difference comparison of gene expression data; processing the gene expression data and miRNA expression data; constructing the miRNA-gene interaction matrix; calculating a miRNA-gene correlation coefficient, obtaining a miRNA-gene correlation matrix, performing fuzzy clustering on the miRNA; constructing a combined miRNA-gene interaction matrix and a miRNA-gene correlation matrix, calculating absolute average correlation degree of the gene with each miRNA, adding the gene into the miRNA according to absolute average correlation degree for constructing the miRNA-gene regulating module; calculating the correlation degree of the miRNA in each module, and ordering according to the correlation degree. The main process is presented in a graph 1. The method can be used for acquiring the cancer-related miRNA for searching the function and the mechanism in a cancer development and generating process, screening the miRNA biological mark in cancer early-period diagnosis, and acquiringtargets in targeted treatment of the cancer.

A system and method for reconstructing pathways in large genetic networks from genetic perturbations comprises an analysis method and system that applies a recursive algorithm for determining the path between every gene pair in an arbitrarily large genetic network from large-scale gene perturbation data and reconstructs all direct and indirect regulatory gene interactions in the network. Graph theory mathematics is applied to genetic network reconstruction in the following manner: Genetic perturbation data is used to identify all genes accessible from a perturbed gene to generate an accessibility list for the gene. Graph theory mathematics is applied to the accessibility list and its graph to determine a condensation of the graph as defined by the condensation's accessibility list. Graph theory mathematics is applied to the accessibility list, such as through a recursive algorithm performed on a desktop computer, to obtain an adjacency list for the gene that characterizes a genetic network.

The invention discloses an analysis method for predicting body weight increase caused by treating schizophrenia through a second-generation antipsychotic based on the polygene combination interactiveeffect. The method comprises the steps that a sample is prepared for collecting peripheral blood of a patient with body weight increase caused by treating schizophrenia through the second-generation antipsychotic, a hypotonic salt fractionation method is used for extracting a genome DNA sample; a MODLI-TOF flight mass spectrum detecting method is used for performing genetic typing of a 5-HT2CR gene, a histamine 1 receptor gene, an oxytocin gene, an NPY / R gene, a Leptin gene, an adiponectin gene, an FGF21 gene and a FGF23 gene; data analysis and extraction are performed, instrument original data is aligned, data with no noise interference for statistic analysis is obtained, a generalized multi-factor dimension reduction method is used for performing the quantitative trait gene-gene interaction effect, crossed verification is further applied, and the gene interaction effect is used for predicting body weight increase. By adopting the generalized multi-factor dimension reduction method, the continuous ending variable is processed, covariance is introduced, and the method has the advantages of greatly enlarging the application range and greatly increasing the prediction accuracy.

The invention discloses a method and a system of detecting epistasis of a complex disease on the basis of chromatin regulation loops. Chromatin remote-interaction data and chromatin segmentation status data of cell lines related to the complex disease are collected and arranged; the above-mentioned data are utilized to establish the chromatin regulation loops; and SNP (Single nucleotide polymorphism) interaction which is in the regulation loops and can influence phenotypes of the complex disease is calculated. According to the method, the data of chromatin remote-interaction and the like are utilized to establish the chromatin regulation loops based on gene interaction, and the epistasis is calculated according to the chromatin regulation loops. Compared with the prior art, the method cangreatly decrease a calculation amount, can also reduce false negative results, thus rapidly and accurately explores SNP interaction related to the complex disease, and provides potential targets for subsequent drug design and the like.

Microarray technology allows the multiple parallel processing of information generated from matrices of huge numbers of loci on a solid substrate, which is useful in the gathering of gene signatures defining specific biological states. An approach has been developed to facilitate this process wherein genes of the same regulatory modality are selected. The transcriptional regulation of these genes is related to the same control element. Primers specific for the regulatory genes are selected, based on minimum cross-reactivity with other genes, using known gene data banks. PCR products of selected regions of known genes either binding to this sequence or whose expression is dependent on this binding, as well as genes interacting with the regulatable genes and control genes, referred to as “amplicons” or “gene cDNA fragments” of between about 450 and 1000 nucleotide bases in length, are obtained from a total RNA pool. These amplicons are arrayed on a nylon membrane or other appropriate microchip susbstrate, which is then used as a regulatory gene-specific microarray that is hybridized with sample. Sample will typically be the mRNA obtained from cells associated with a particular state (examples include age or exposure to conditions such as outspace, low gravity), disease (such as cancer or an infection), or disorder (such as a genetic defect or trauma). The transcriptionally regulated profile of regulatory gene-related genes specific to a given cultured cell sample is then determined using a software based analysis of the amount of hybridization which is detected. This information is useful in determining drug targets, markers associated with the disease state (either the presence or absence, or the extent of the disease), or the response of the disease state to drugs or other treatments.

The invention discloses a cell metabolism reprogramming method and application thereof, and belongs to the field of genetic engineering.The cell metabolism reprogramming method utilizes sensitive nodes of a cell metabolism network to reprogram the metabolism network and mainly comprises the three parts of CRISPRi-based double-gene combination weakening, cell high-throughput screening and survival rate-based gene interaction analysis. The invention provides an intelligent metabolism reprogramming method which is novel, simple, efficient and low in cost, and can be widely used for operating a cell metabolism network.

The invention provides a cloning and transient expression method of persimmon deastringency related genes. The method comprises: first acquiring gene 3'-terminal sequences, then employing 3' RACE (rapid amplication of cDNA ends) technology to acquire 3'-terminal sequences of ADH and PDC gene family members in persimmon fruits; adopting Q-PCR (quantitative polymerase chain reaction) technology to analyze the genetic expression of ADH and PDC gene family members in a persimmon fruit deastringency treatment; and conducting separation to obtain full-length sequences of ADH and PDC gene family members, then establishing a transient expression system of persimmon leaves. The method of the invention clones the persimmon deastringency related gene family members, analyze the expression patterns of the family members in the persimmon deastringency treatment, and finally verifies functions of the target genes through transient expression of the persimmon leaves. The invention clarifies the regulation mechanism for postharvest persimmon deastringency from the molecular mechanism aspective, and can be used for further functional verification (transgenosis, gene interaction and the like) study of the postharvest persimmon deastringency mechanism.

The invention discloses the application of rice tRNA isopentenyl transferase gene OsIPT9 in rice resistance to brown planthopper. It belongs to the field of plant genetic engineering technology. OsIPT9 It has the amino acid sequence shown in SEQ ID No.1, the nucleotide sequence shown in SEQ ID No.2, and the ORF sequence shown in SEQ ID No.3. Through Agrobacterium-mediated genetic transformation, the OsIPT9 Transplanted into Nipponbare, which is susceptible to N. lugens, the overexpressed plants have enhanced resistance to N. lugens; at the same time, the resistant material NIP‑Bph6‑NIL was knocked out by CRISPR / Cas9 technology OsIPT9 , resulting in a significant down-regulation of plant resistance to N. lugens. The gene of the invention provides a good theoretical basis for studying the gene interaction between rice and brown planthopper, and has reference significance for studying gene molecular function and breeding.