65 results about "Gene list" patented technology

The invention discloses a pharmaceutical activity prediction and selection method based on genetic expressions and drug targets. The method comprises following steps: 1) obtaining target genes corresponding to drugs to be detected according to information in drug target database; obtaining genetic expression data of disease tissues of patients and corresponding compression data and obtaining important genetic lists of morbidity processes of patients by evaluating importance of genes through a systems biology method; 2) searching for whether the target genes obtained in the step 1) target the important gene lists during mobility of the patients or not through statistical analysis of in order to predict pharmaceutical activity of patients and select drugs suited to patients. The method is easily used with high efficiency and broad application scope. The prediction method can be used for selecting drugs suitable for individual patients such that a personalized treatment schme can be provided for patients.

The present invention provides methods for preparing a gene expression profile of a breast cancer cell, tumor, or cell line, where the gene expression profile may be evaluated for one or more gene expression signatures indicative of multidrug resistance. The signature may be indicative of resistance to one or more chemotherapeutic agents selected from a Taxol (e.g., Docetaxel or Paclitaxel), an antibiotic (e.g., Doxorubicin or Epirubicin), an antimetabolite (e.g., Fluorouracil and/or Gemcitabine), and an alkylating agent (e.g., Cyclophosphamide). Generally, the gene expression profile contains the level of expression for a plurality of genes listed in FIGS. 3, 4, and/or 5. Gene expression profiles for evaluating multidrug resistance for ER positive and ER negative breast cancers are also provided.

The present invention relates to a Mycoplasma hyopneumoniae vaccine strain comprising a mutation in at least one of the genes listed or as deposited with the National Measurements Institute (Australia) under accession number NM04/41259, which strain is temperature sensitive and attenuated, a vaccine comprising such strains and methods and uses thereof.

Colon cancer cells in a sample are screened by analyzing the amount of expression of at least 2 or more genes or products thereof selected from the group of genes listed in Tables 1 and 30. As compared to conventional method, patients having colon cancer can be detected with higher accuracy. Colon cancer cells in stool are also screened by analyzing expression of genes selected from the group of genes listed in Table 37.

A method for determining pulmonary fibrosis subtype and/or prognosis in a subject having pulmonary fibrosis comprising: a. determining an expression profile by measuring the gene expression levels of a plurality of genes selected from genes listed in Table 1, 2, 3, 4 7, 8, 9, and/or 10, in a sample from the subject; and b. classifying the subject as having a good prognosis or a poor prognosis based on the expression profile; wherein a good prognosis predicts decreased risk of post lung transplant primary graft dysfunction, and wherein a poor prognosis predicts an increased risk of post lung transplant primary graft dysfunction.

The present invention relates to extraction of human tissue kallikrein, which is a separation and purification method of gene expressed human tissue kallikrein protein, and its operation is as follows: (1). supernatant separation; (2) chromatography; 1). step gradient elution; firstly, using buffer solution with 20-30mM and pH 7-8 to balance column, then pumping the supernatant into the column; using buffer solution containing 0.1-0.2 M of NaCl to make elution, then using the buffer solution containing 0.3-0.5 M of NaCl, collecting fraction for stand-by; firstly, using NaAc with 10-20 mM and pH 5.0-6.0 to balance column, then making step gradient elution and collecting fraction; and making linear gradient elution, in eluent salt component range is 0.1M NaCl to 0.5M NaCl, collecting fraction and storing; (3). utilizing affinity chromatography to make separation and purification.

A system for characterizing intercellular communication and heterogeneity in cancer tumors, and more particularly a method for detecting sub-populations and receptor-ligand states for providing predictive information in relation to cancer and cancer treatment is disclosed. The system comprises the steps of obtaining from a NGS sequencer, single-cell RNA-seq for a plurality of cells within a tumor, correlation with a plurality of data sets from a curated gene list of receptor-ligand pairs, normalizing their transcript abundance data, assigning states (e.g. 0,1,2,3) to each curated receptor-ligand pair in each cell (e.g. depending on {L:R}={0:0, 0:1, 1:0, 1:1}), thereby forming a matrix of receptor-ligand states, extracting sub-groups from the matrix that are not invariant and applying unsupervised clustering methods to identifying sub-clusters, identifying sub-populations within the set based on pair-wise distances between individual cells and similarity of cellular transcriptomes, identifying expressed ligands and receptors across the sub-populations, cross-referencing against the curated set of receptor-ligand pairs and providing a visually display the results by a mapping module for the clinician. The method can be used to study intercellular communication to elicit the etiology of diseases, and can be used to measure the disruption of intercellular communication to diagnose similarly disrupted disease patterns across patients.

Methods for the diagnosis of leukemias, and more specifically AML, such as MLL-AF9 AML, in a subject, based on the assessment of the expression or activity of one or more of the genes listed in Tables 1 and 2 are disclosed. The use of antibodies or antigen-binding fragments thereof that bind to one or more of proteins showing preferential expression at the cell surface of AML leukemic cells for treating AML is also disclosed.

The invention discloses a traditional Chinese medicine (TCM) active ingredient forecasting method excavated on the basis of pathway modes. The traditional Chinese medicine active ingredient forecasting method includes the following steps of collecting data of compound ingredients with Chinese Academy of Sciences (CAS) registry numbers in TCM, collecting associated genes of compounds to form compound-gene associated pairs and sorting the genes according to occurrence frequency of the associated genes to form an associated gene list, setting a threshold value to screen frequent genes to form biological pathway data sets and enable each frequent gene to correspond to one biological pathway data record, excavating the pathway modes for the biological pathway data sets, grading the frequency genes, grading activity of the compounds, and setting threshold values for scores of the genes and scores of the activity of the compounds. The compound-gene associated pairs are screened according to the threshold values. The remaining compounds are reserved. Consequently, active ingredients of the TCM can be forecasted.

The current invention relates to new tools and methods enabling neuroblastoma patient stratification into prognostic favorable or unfavorable groups. The invention is based on the re-analysis of published gene expression data-sets studying neuroblastoma tumors generating different prognostic gene lists. The overlapping gene lists were subsequently tested for their prognostic power on both the published tumor samples and on an unseen large set of unpublished samples, greatly increasing the statistical power of prognostic analyses. In addition, expression analysis of miRNAs in neuroblastoma tumors with different prognosis was performed. By doing this, the inventors could establish a neuroblastoma prognostic classifier with highly improved prognostic power, which is independent from the tumor sample set used to establish it. This classifier and its related prognostic tools and methods are thus perfectly suitable for routine clinical assessment of neuroblastoma prognosis.

The invention relates to the use of inhibitors of the expressed proteins of the murine genes and/or their human homologues listed in Table 1 for the preparation of a therapeutical composition for the treatment of cancer, in particular for the treatment of solid tumors of lung, colon, breast, prostate, ovarian, pancreas and leukemia and the use of the genes listed in Table 1 for the diagnosis of cancer. The invention also relates to the therapeutical compositions comprising the inhibitors and to methods for development of the inhibitor compounds.

The invention discloses a RapMap method for rapid and high-throughput positioning and cloning of a plant QTL gene. The method comprises the steps of: selecting strains with relatively small characterdifferences from the core germplasm as gradient parents; constructing as many F2 gradient genetic populations as possible; preliminarily positioning QTL by performing chip detection or next-generationsequencing on two separated extreme phenotypic DNA pools of each group, verifying the QTL at the single plant level of each gradient group according to the co-separation criteria provided by the invention, and cloning a target gene by using a QTL heterozygous family as a near-isogenic line for fine positioning. The concept of gradient genetic populations and the idea of co-segregation criteria are the core of the invention. Six rice grain length and grain width genes are successfully cloned by applying the RapMap method, and the RapMap is indicated to be a rapid and high-throughput gene cloning RapMap method integrating QTL positioning, verification and near-isogenic line screening into a whole.

Colon cancer cells in a sample are screened by analyzing the amount of expression of at least 2 or more genes or products thereof selected from the group of genes listed in Tables 1 and 30. As compared to conventional method, patients having colon cancer can be detected with higher accuracy.

The invention discloses a method for identifying a cancer driver gene by using a consensus prediction result. The method comprises the following steps: S1, receiving a mutation annotation format (MAF) file as input; S2, processing all the preprocessed input mutation data so as to respectively obtain a candidate driver gene list of each strategy; S3, on the basis of each differential driving gene list, obtaining a common driving gene list by using a rank integration method RobustRankAggreg; S4, evaluating the performance of the result by using Top-N-Precision and Top-N-nDCG, and carrying out KEGG pathway and gene ontology analysis on the common driver gene; S5, obtaining a consensus driving gene list by using an RAA algorithm; S6, employing the SuperExactTest and the Circos for organizing a visualization result. The method has certain superiority in driver gene prediction, although height difference exists between different driver gene identification strategies, not only can the most reliable driver gene be identified through cross analysis of results of each independent strategy, but also potential novel driver genes with undefined features can be found.

There is described herein a method of prognosing endocrine-only treatment in a subject with breast cancer, the method comprising: a) providing a tumor sample of the breast cancer; b) determining the expression level of at least 40 of the genes listed in Table 4 in the tumor sample; c) comparing said expression levels to a reference expression level of the group of genes from control samples from acohort of subjects; and d) determining the residual risk associated with the breast cancer; wherein a statistically significant difference or similarity in the expression of the group of genes compared to the reference expression level corresponds to a residual risk associated with breast cancer.

This disclosure relates to systems and methods that identify, predict, and rank immunogenic T-cell epitopes. In particular, this disclosure identifies epitopes that arose from disease-associated mutations, wherein the epitopes are predicted to elicit immune response from T cells. Specifically, this disclosure simultaneously considers peptide-level information, including MHC Class I and II presentation, helper and cytotoxic T cell response and sample-level information, including mutation clonality and MHC allele dosage. In some embodiment, the systems and methods are used for personalized treatment of cancers.