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203 results about "Gene sets" patented technology

Crop whole genome phenotype prediction method and system fused with environmental indicator gene

PendingCN120656542ABiostatisticsBiological modelsGenome alignmentGene expression level
The invention relates to the technical field of bioinformatics, and provides a crop whole genome phenotype prediction method and system fused with an environmental indicator gene, and the method comprises the following steps: collecting re-sequencing data, and carrying out genome comparison to obtain variation site data; performing whole genome association analysis by using the variation site data to obtain phenotype association site information; carrying out gene expression quantity measurement on samples of the crop population material in different environments to obtain gene expression quantity data; performing differential expression analysis on the gene expression quantity data to screen environmental indicator genes to obtain an environmental indicator gene set; constructing a phenotype prediction model of double-branch fusion; and predicting a to-be-predicted material through the phenotype prediction model to obtain phenotype prediction results for different environments. According to the method, environmental factors are incorporated into the whole genome selection model, so that the phenotype prediction precision in different environments is improved.
Owner:CHINA AGRI UNIV

Construction method and equipment of predictive cell aging model, medium and program product

The invention provides a construction method of a predictive cell senescence model, a method for predicting the senescence state of a tissue sample based on the senescence model, a method for screening potential therapeutic drugs, equipment, a medium and a program product, and relates to the field of intelligent medical treatment. The model construction method comprises the following steps: acquiring a training set sample expression profile data set; identifying a key senescence gene set from the data set by using a feature selection algorithm; inputting the key senescence gene set into a machine learning model to fit a prediction model, and determining an optimal hyper-parameter to obtain a cell senescence model containing the weight of a single gene in the key senescence gene set; the cell senescence model is a senescence score obtained by calculating the sum of the product of the expression quantity of a single gene and the regression coefficient thereof. The cell senescence model, namely PreCSenM, is constructed by integrating a plurality of senescence characteristic gene sets and a gene scoring algorithm, the accuracy in CS evaluation is superior to that of 10 existing methods, and the application of CS from biological research to clinical scenes is also realized.
Owner:INSTITUTE OF BASIC MEDICAL SCIENCES CHINESE ACADEMY OF MEDICAL SCIENCES

Method and system for clustering transcriptome sequencing data

The invention provides a clustering method and system for transcriptome sequencing data. The method is applied to the technical field of data processing, and comprises the following steps: collecting cervical adenocarcinoma and para-carcinoma tissue specimens of a plurality of patients, and carrying out data preprocessing to obtain a standardized gene expression matrix; performing clustering operation on the standardized gene expression matrix based on a clustering analysis method combining a potential category model and sub-alliance division to obtain a clustered gene set; performing gene function annotation on the clustered gene set, and performing correlation analysis on a clustering result after function annotation and clinical characteristics of cervical adenocarcinoma to obtain correlation between gene expression and the clinical characteristics; and on the basis of clustering analysis and correlation analysis results, constructing a deep clustering prediction model based on a variational auto-encoder and a Gamma hybrid model so as to predict the prognosis risk or chemotherapy sensitivity of the patient. The problems that high-dimensional transcriptome data is poor in clustering stability and low in prognosis prediction precision are solved.
Owner:THE AFFILIATED HOSPITAL OF SOUTHWEST MEDICAL UNIV +1

EGFR wild-type lung adenocarcinoma prognosis risk assessment method based on multi-omics and machine learning

The invention provides an EGFR wild-type lung adenocarcinoma prognosis risk assessment method based on multi-omics and machine learning, and the method comprises the steps: obtaining multi-omics and clinical data of lung adenocarcinoma, obtaining a data set, and carrying out the multi-omics consensus clustering, and obtaining a molecular typing result; high-risk subtype specific candidate genes are identified, a candidate prognosis gene set is obtained, multi-algorithm machine learning comparison optimization is carried out, and a modeling strategy is obtained; performing feature screening and model training to obtain a multi-omics feature model so as to calculate an individual risk score of the to-be-tested sample; the individual risk score and the clinical staging information are utilized to obtain a clinical column diagram and a survival prediction result, then the flow of the multi-omics feature model, the individual risk score and the survival result is Web to obtain a clinical system, and a lung adenocarcinoma prognosis risk assessment result is output. The invention can realize an objective, accurate, generalizable and multifunctional prognosis evaluation and treatment guidance tool, and has important clinical application value and wide industrialization prospect.
Owner:XIEHE HOSPITAL ATTACHED TO TONGJI MEDICAL COLLEGE HUAZHONG SCI & TECH UNIV

Intelligent tumor microenvironment analysis and drug screening method based on multi-modal data

The invention discloses an intelligent tumor microenvironment analysis and drug screening method based on multi-modal data, and relates to the field of tumor research. The method comprises the following steps: obtaining a plurality of prognosis image features according to preoperative magnetic resonance images of the brain of a plurality of glioblastoma patients; identifying a key image genomics gene set for each prognostic image feature; analyzing biological reasons of prognosis differences of high-risk patients and low-risk patients by using a transcriptome method; analyzing biological functions of prognosis image features; utilizing Fisher to accurately test and determine a cell population associated with the prognostic image features; determining a functional state of the cell population based on the scRNA-seq data of the cell population; constructing an image-gene-cell population-functional state association; potential therapeutic drugs for cell populations associated with prognostic image features are parsed using chi-square test. According to the invention, the tumor heterogeneity of glioblastoma can be depicted from the perspective of images, and potential therapeutic drugs can be identified.
Owner:HARBIN MEDICAL UNIVERSITY

Emblycoris indica phytase gene set and application thereof in aspect of RNAi (Ribonucleic Acid Interference)-mediated pest control

The invention belongs to the technical field of green prevention and control of agricultural pests, and particularly relates to application of a phytase gene set of orius guttatus in the aspect of RNAi-mediated pest prevention and control. The gene set comprises a gene RP382, a gene RP382L1, a gene RP382L2 and a gene RP382L3, amino acid sequences of proteins coded by the gene RP382, the gene RP382L1, the gene RP382L2 and the gene RP382L3 are sequentially shown as SEQ ID NO: 5-8, and nucleotide sequences of the gene RP382, the gene RP382L1, the gene RP382L2 and the gene RP382L3 are sequentially shown as SEQ ID NO: 1-4. According to the invention, through systematic analysis, four phytase gene family members are identified in the Eriomycorus lividus for the first time, and the phytic acid metabolism capability of pests is destroyed by interfering the expression of the genes, so that the death rate of the pest Eriomycorus lividus is obviously increased to 50%.
Owner:SANYA INSTITUTE OF NANJING AGRICULTURAL UNIVERSITY +1

Training method of respiratory tract infection disease progress and prognosis prediction model

The invention relates to a training method of a respiratory tract infection disease progress and prognosis prediction model. The training method comprises the following steps: extracting mRNA from peripheral blood of a target patient, and carrying out transcriptome sequencing to obtain a sequencing result; based on the ferroptosis related gene set, comparing ferroptosis score differences of two groups of patients with community-acquired pneumonia and sepsis, and screening corresponding ferroptosis related genes with statistical significance from a sequencing result; screening out genes meeting preset conditions from the ferroptosis related genes based on LASSO regression; and establishing an RTI clinical outcome prediction model through logistic regression by taking whether the patient is sepsis or not as an outcome dichotomy variable and taking the screened gene expression quantity as a prediction variable. According to the invention, after the prediction model is subjected to machine learning screening such as LASSO and the like, the core feature with the highest prediction value is reserved, so that the risk of over-fitting of the model on training data is reduced.
Owner:PEKING UNION MEDICAL COLLEGE HOSPITAL

Application of Ki-67 protein, CHG protein and CTGF protein or detection substances thereof

The invention relates to the field of disease diagnosis, and particularly discloses application of Ki-67 protein, CHG protein and CTGF protein or detection substances thereof in preparation of products for tumor subtype classification, and the tumor is olfactory neuroblastoma. Representative molecular markers which correspond to various NBM types, can be verified by IHC staining and are limited in number are screened out from an ONB NBM trityping gene set obtained by an scRNA sequencing technology, and a simple optimization scheme which aims at the ONB NBM trityping and is suitable for clinical examination and classification is established through FFPE clinical queue verification.
Owner:EYE & ENT HOSPITAL SHANGHAI MEDICAL SCHOOL FUDAN UNIV

Lung adenocarcinoma prognosis prediction model based on heme metabolism related genes, construction method and application

The invention discloses a lung adenocarcinoma prognosis prediction model based on heme metabolism related genes and a construction method and application thereof. According to the invention, a heme metabolism related gene set is screened through a molecular characteristic database, and a gene significantly related to prognosis is screened by using transcriptome and clinical data of lung adenocarcinoma in a TCGA database and combining single-factor Cox regression, LASSO regression and multivariable Cox analysis. And through multi-time iterative modeling, selecting high-frequency stable genes and corresponding regression coefficient mean values to construct a heme metabolism risk score. According to the method, a random survival forest model is adopted to carry out iteration evaluation on gene importance for multiple times, the first 50% of genes which have the maximum influence on the model are screened, and finally the five important characteristic genes related to the heme metabolism risk are identified by taking an intersection with an LASSO result. The application provides new theoretical basis and technical support for precise treatment of lung adenocarcinoma, and has important clinical application value.
Owner:BEIJING CANCER HOSPITAL PEKING UNIV CANCER HOSPITAL

Method, device and equipment for identifying communication relationship between cells and storage medium

The invention discloses a method, a device and equipment for identifying a communication relationship between cells, and a storage medium, and relates to the technical field of bioinformatics, direct causal contribution between the cells is quantified by using a causal association relationship of a source cell gene to a target cell gene, the communication relationship between the cells can have explanatory force at a causal level, and the identification accuracy of the communication relationship between the cells is improved. Further, the overall regulation effect among the cell populations is accurately evaluated. The method comprises the following steps: acquiring gene expression data of different cell types, wherein the different cell types at least comprise source cells and target cells; aiming at the candidate genes of the target cell, constructing different hypothesis models by using the covariable gene set, and determining a causal association relationship between the source cell gene and the target cell gene through the different hypothesis models; and calculating the communication intensity of the source cell to the target cell according to the causal association relationship of the source cell gene to the target cell gene, so as to identify the causal regulation relationship between the cells through the communication intensity.
Owner:HANGZHOU INST FOR ADVANCED STUDY UCAS

Chronic pancreatitis complication risk grading system based on exosome transcriptome data

The invention relates to the technical field of medical biology, in particular to a chronic pancreatitis complication risk grading system based on exosome transcriptome data, and aims to solve the problems that existing chronic pancreatitis (CP) typing lacks molecular basis, complication risk prediction is weak and clinical transformation is poor. According to the system, plasma exosomes are extracted and sequenced, a functional characteristic gene set is constructed in combination with pancreas single cell data, CP is divided into three risk increasing subtypes by using a COCA algorithm, and finally 12 core miRNAs are screened to construct a BPNN diagnosis model. The invention proves that the plasma exosome can be used for staging classification of chronic pancreatitis for the first time, miRNA non-invasive accurate layering illness conditions can be detected through qPCR, the risk of fatty diarrhea and 3c type diabetes mellitus can be predicted, and the non-invasiveness, convenience, classification accuracy and result repeatability of the plasma exosome have clinical application and transformation advantages.
Owner:THE NAVAL MEDICAL UNIV OF PLA

Cell type identification

Provided herein are compositions and methods for identifying the cell type origin of cells based on RNA sequencing (RNA-seq) data.The method provided herein may include: receiving a plurality of sequencing read counts; providing a set of detected cell types and a related gene set G for each cell type, such that each gene set G comprises a plurality of genes g; scoring the sequencing read counts to generate an assignment score; and assigning each cell among the plurality of cells to the cell type with the highest assignment score, thereby identifying the cell type origin of each cell.This method can be implemented, for example, using a computer system.
Owner:SANOFI SA(FR)

Method and system for constructing renal clear cell carcinoma prognosis model based on metabolic gene set

The invention belongs to the technical field of biomedicine, and particularly relates to a renal clear cell carcinoma prognosis model construction method and system based on a metabolic gene set. The system comprises: a metabolic gene set data acquisition module for acquiring metabolic gene set data of a patient with renal clear cell carcinoma, the metabolic gene set data including CYP3A7, ST3GAL5, DBH, UGT2B7, GCNT4, LIPA, ITPKB, HS3ST1, GYG2, and CYP51A1; the survival time calculation module is used for calculating the survival time of the renal clear cell carcinoma patient based on the prediction model; the prediction model comprises a formula I for calculating the risk score of the patient and a formula II for calculating the survival probability of the patient at a certain time point; and the result output module is used for outputting a prognosis result of the patient based on the survival time of the renal clear cell carcinoma patient. The system can significantly improve the accuracy and reliability of prognosis of ccRCC patients, and has wide application prospects and commercial values.
Owner:PEOPLES HOSPITAL OF HENAN PROV

Cross-animal general skeleton-derived hematopoietic stem cell marker gene set and screening method thereof

The invention belongs to the technical field of biomolecular markers, and particularly relates to a cross-animal general skeleton-derived hematopoietic stem cell marker gene set and a screening method thereof. According to the invention, a bone-derived hematopoietic stem cell marker gene set universal across animal categories is constructed for the first time, and the bone-derived hematopoietic stem cell marker gene set comprises at least five of Cdc42, Cbx, Tfam, Denr, Mcts1, Ak2, Ruvbl, Ahcy, Nna and Vdac; the hematopoietic stem cell marker gene set is obtained through cross-species homologous gene screening, the defect that a traditional vertebrate marker has no orthohomology in invertebrates is overcome, accurate recognition of HSC in shells is achieved, the hematopoietic stem cell marker gene set has species universality and cell specificity, the immune state of aquatic animals can be evaluated, disease-resistant breeding can be guided, and the application prospect is wide. And molecular evidence is provided for analyzing an evolution path of a hematopoietic system from invertebrates to vertebrates.
Owner:OCEAN UNIV OF CHINA

Rural IP hatching method, device and IP hatching system

The invention provides a country IP incubation method and device and an IP incubation system, and the method comprises the steps: obtaining the cultural data of a country, wherein the cultural data comprises the text cultural data, the visual cultural data and the audio cultural data; feature vectors of the culture data are extracted and fused, and a multi-modal culture feature matrix is generated; performing culture gene analysis on the multi-modal culture feature matrix to obtain a gene set which contains symbol vectors, mental prototype vectors and corresponding culture gene entropy values; and creating a rural IP incubation scheme according to the gene set. According to the technical scheme, the technical problems that in the prior art, data integration is low in efficiency, core element screening subjectivity is high, and market verification is lagged in rural culture IP development can be effectively solved.
Owner:ABC FINANCIAL TECH CO LTD

A method for inferring gene regulatory network combining information theory and machine learning

ActiveCN115188416BEnsemble learningBiostatisticsComputation complexityGene Expression Process
The application discloses a gene regulation network inference method combining information theory and machine learning, including obtaining time series of different gene expression processes, converting the time series into symbol sequences, calculating the symbol transition entropy between different gene symbol sequences, calculating the regulation gene set of each gene, constructing a model for the time series of a target gene and the time series set corresponding to the regulation gene set of the target gene and training the model, calculating the importance score of the regulation gene, screening the regulation gene with the importance score meeting a first threshold value and adding the regulation gene into a core regulation gene set; obtaining the symbol transition entropy of all core regulation genes to the target gene, combining the importance score and the symbol transition entropy of the core regulation gene into a regulation coefficient after normalization, screening the core regulation gene set meeting a second threshold value, and obtaining the core regulation gene set of all target genes. The method reduces the calculation complexity, solves the overfitting problem of the model based on machine learning, and improves the prediction accuracy.
Owner:DALIAN MARITIME UNIVERSITY

Web-based single-cell RNA sequencing data intelligent analysis system and method

The invention provides a Web-based single-cell RNA sequencing data intelligent analysis system and method. The method comprises the following steps: receiving a cell group through a Web interface; performing differential gene analysis on the single-cell RNA sequencing data contained in the cell group to obtain an original differential gene list, and filtering the original differential gene list by adopting a multi-threshold screening algorithm to obtain a target differential gene list; performing species automatic identification processing on the target differential gene list, calling a target local gene set database based on a result of the species automatic identification processing, and performing parallel enrichment analysis independent of network connection on the target differential gene list according to the target local gene set database to obtain a gene enrichment analysis result; and generating an interactive chart by adopting an intelligent label anti-overlapping algorithm so as to visualize the interactive chart. According to the method, the problems of high operation threshold, low batch analysis efficiency, unstable result and poor interactivity in the prior art are solved.
Owner:WOMEN & CHILDRENS MEDICAL CENTER AFFILIATED WITH GUANGZHOU MEDICAL UNIVERSITY

Detection method and system for social anxiety disorder risk assessment

The invention relates to the technical field of biomedical detection and bioinformatics, and discloses a detection method and system for social anxiety disorder risk assessment, and the method comprises the steps: obtaining transcriptome data of a peripheral blood sample of a to-be-detected object, and carrying out preprocessing and normalization to obtain a standardized gene expression matrix; extracting minimum gene set expression data containing 10 genes such as HSF5 and FADS2, and performing Z-score standardization processing by using the solidified model parameters; calling a preset weight coefficient and an intercept item to perform linear weighting and probability conversion calculation on the standardized data to obtain a disease prediction probability of the subject; and carrying out risk layering according to the optimal critical value and generating an auxiliary diagnosis report. According to the method, stable features are screened through a machine learning algorithm, the scoring model is constructed, subjectivity of traditional clinical diagnosis is overcome, and objective, quantitative and automatic evaluation of social anxiety disorder risks is achieved.
Owner:HEBEI UNIVERSITY

Method for biosynthesizing ginsenoside by using tobacco BY-2 cells as chassis

The invention discloses a method for biosynthesizing ginsenoside by taking tobacco BY-2 cells as a chassis, and belongs to the technical field of bioengineering. The method comprises the following steps that firstly, a recombinant expression vector containing a ginsenoside synthesis pathway key gene set is constructed, and the gene set comprises genes such as tHMGR, SE and SS from ginseng and Pn1-31 and Pn3-31 genes from panax notoginseng; secondly, introducing the recombinant vector into tobacco BY-2 cells, and screening through a solid culture medium to obtain a pure positive cell line; and finally, culturing the positive cell line in a liquid or solid culture medium to obtain ginsenoside Rh2 and / or Rg3. By utilizing the advantages of fast growth and stable culture of the tobacco BY-2 cells, a rare ginsenoside synthesis pathway is successfully reconstructed, efficient heterologous synthesis of the rare ginsenoside is realized, and a repeatable technical scheme is provided for industrial production of the rare ginsenoside.
Owner:ZHEJIANG FINDYOU BIOTECHNOLOGY CO LTD

Method and system for mining potential proto-oncogenes based on chromatin three-dimensional structure

The present invention discloses a method and system for mining potential proto-oncogenes based on the three-dimensional structure of chromatin, which relates to the field of computational biology technology. The method comprises: obtaining multiple mutation insulation regions based on chromatin data and cancer mutation data, and inputting the regions into a trained binding site predictor to obtain prediction results and destroyed insulation regions; obtaining multiple differentially expressed gene sets based on cancer gene expression data, intersecting the multiple differentially expressed gene sets to obtain a final differentially expressed gene set; intersecting the final differentially expressed gene set and the genes in the destroyed insulation regions to obtain intersection genes; performing survival analysis to obtain analysis results, screening the intersection genes based on the analysis results to obtain genes associated with poor prognosis; and screening the intersection genes to obtain potential proto-oncogenes. This improves the accuracy and reliability of mining potential proto-oncogenes while saving time and economic expenses.
Owner:XIDIAN UNIV

Probe design method and system for multi-round space transcriptional group imaging

The invention discloses a probe design method and system for multi-round space transcriptional group imaging, and relates to the technical field of bioinformatics, and the probe design method comprises the following steps: constructing a retrieval database; the method comprises the following steps: traversing a known RNA (Ribonucleic Acid) sequence to obtain target sections of all isoforms of the same gene, preprocessing the target sections, dividing an obtained candidate probe sequence into two sections, carrying out additional non-specific detection to obtain target probe sequences of all isoforms, and screening according to all expression matrixes in a retrieval database to obtain target region probes; the method comprises the following steps: generating a plurality of random sequences through random ATCG, preprocessing, and designing a non-targeted region probe according to the random sequences; obtaining a single cell expression matrix from the retrieval database, and optimizing the cell type level expression quantity variance of a given gene set among different imaging rounds to be minimum based on a simulated annealing algorithm to obtain a gene codebook; according to the probe design method and system, the overall capture efficiency of the probe is improved to a certain degree, and meanwhile various coding strategies are compatible.
Owner:ARTIFICIAL INTELLIGENCE RES INST OF HEFEI COMPREHENSIVE NAT SCI CENT (ANHUI ARTIFICIAL INTELLIGENCE LAB)

Method, device and system for identifying high gene module scoring area

The invention discloses an identification method, device and system for a high gene module scoring area, and relates to the technical field of space transcriptomics. The identification method comprises the following steps: acquiring space transcriptome data, dividing cells into a plurality of unit grids according to space coordinate information of the cells, and determining corresponding grid space coordinates for each unit grid; calculating a module score value of each cell and determining a high-score cell set; calculating an integrated gene set scoring index; and carrying out region division on the unit grid and determining a high gene module scoring region. According to the method, a plurality of genes are analyzed as a functional whole, the limitation that traditional single-gene analysis cannot reveal collaborative regulation is overcome, spatial quantization of a gene set synergistic effect is realized, and the problem that a gene set enrichment region cannot be positioned in the prior art is solved.
Owner:KANGMEIHUA GENE TECH CO LTD

A prostate cancer biochemical recurrence prognosis risk prediction model based on fatty acid metabolism and cancer cell stemness genes and a construction method thereof

PendingCN122392918AcDNA libraryCancer cell
The application provides a prostate cancer biochemical recurrence prognosis risk prediction model based on fatty acid metabolism and cancer cell stemness genes and a construction method thereof, wherein the construction method comprises the following steps: S1: data collection: obtaining prostate cancer sample transcriptome data with biochemical recurrence information from a database, and dividing the data into a model training set and a model test set; S2: stemness score analysis; S3: fatty acid metabolism score analysis; S4: based on the analysis results of S2 and S3, identifying a co-expression gene module related to fatty acid metabolism and stemness characteristics in prostate cancer by a co-expression similarity algorithm and a hierarchical clustering algorithm, and obtaining a fatty acid metabolism and stemness-related gene set; S5: constructing a prostate cancer BCR prognosis risk prediction model; S6: constructing a nomogram model; S7: extracting RNA of a to-be-tested sample, constructing a cDNA library, quantifying the expression of the above genes, and calculating the prognosis risk level of prostate cancer through the expression level.
Owner:NANTONG UNIV

Diffuse large B-cell lymphoma genotype classification method, device and storage medium

The embodiment of the present application discloses a genotype classification method for diffuse large B-cell lymphoma, a computer device, and a computer-readable storage medium. The method includes the following steps: testing a sample according to a preset specific gene set to obtain variation detection data; preprocessing the variation detection data to obtain variation information; generating an initial feature matrix based on the variation information, screening the initial feature matrix to obtain a feature matrix, and the feature matrix is ​​used to characterize the gene variation contained in the specific gene set in the corresponding sample; obtaining a first genotype label and an important feature set, constructing a data set based on the feature matrix, the first genotype label, and the important feature set, and training a classification model; obtaining a second genotype label output by the classification model, and determining a genotype classification report based on the second genotype label. Therefore, the present application can reduce the cost of testing, can effectively predict the patient's genotype, and has a high clinical application value.
Owner:GUANGZHOU KINGMED CENTER FOR CLINICAL LABORATORY CO LTD +1

Modeling method and device for m6A methylation level visual model

The invention discloses an m6A methylation level visual model modeling method and device, and relates to the field of biomedicines.The m6A methylation level visual model modeling method comprises the steps that expression quantities of three gene sets, obtained after genes related to m6A methylation are standardized, in single cells of a sample to be detected are mapped to three coordinate axes of a ternary phase diagram; the distribution condition of the gene set expression quantity in the ternary phase diagram after the gene related to m6A methylation in the single cell of the sample to be detected is standardized is obtained, and the m6A methylation level of the single cell of the sample to be detected can be visually seen through the corresponding distribution area of the ternary phase diagram; expression of multiple genes which have different functions and are related to single cell m6A methylation can be unified under the coordinate axis of the same ternary space, and a reasonable, quantifiable and explainable model is formed, so that the cell m6A methylation degree is indicated.
Owner:RENMIN HOSPITAL OF WUHAN UNIVERSITY (HUBEI GENERAL HOSPITAL)

Feature gene selection method and system based on deep learning attribution analysis and beam combination optimization

The invention provides a feature gene selection method and system based on deep learning attribution analysis and beam combination optimization, and relates to the technical field of signal analysis, and the method comprises the following steps: obtaining single cell RNA sequencing data and batch RNA sequencing data; the method comprises the following steps: based on single-cell RNA sequencing data, obtaining an initial gene pool aiming at a plurality of disease subtypes through a consensus screening strategy fusing XGBoost multi-dimensional importance measurement and deep learning SHAP attribution analysis; performing first-stage optimization on the gene list of each subtype by taking the initial gene pool as a starting point and adopting beam combination search and based on a global discrimination objective function to obtain a first-stage optimized gene set; integrating the first-stage optimized gene set with the differential expression gene set of the batch RNA sequencing data, and carrying out second-stage optimization by adopting bundle combination search again to obtain a second-stage optimized gene set; and performing cross validation integration on the second-stage optimized gene set, and outputting a final feature gene set.
Owner:NANKAI UNIV

Single cell transcriptome data processing method and device, parameter library and electronic equipment

The embodiment of the invention discloses a single cell transcriptome data processing method and device, a parameter library and electronic equipment, and the method comprises the steps: obtaining a common parameter, the common parameter comprises a reference feature gene set and a reference association relationship between an original feature and an extracted feature, the reference feature gene set comprises a plurality of feature genes, and the reference association relationship comprises a reference association relationship between the original feature and the extracted feature; the reference association relationship is used for dimension reduction processing of a gene expression condition; based on the reference feature gene set and the single cell transcriptome data of the to-be-detected sample, determining the gene expression condition of the feature gene in the to-be-detected sample; on the basis of the gene expression condition of the feature gene in the to-be-detected sample and the reference association relationship, performing first data dimension reduction processing to obtain a first dimension reduction result; wherein the to-be-detected sample and the common parameters belong to the same biological tissue type. By adopting the embodiment of the invention, the computing resource demand can be effectively reduced, and the data processing efficiency is improved.
Owner:BEIJING DINGCHENG PEPTIDE SOURCE BIOINFORMATION TECHNOLOGY CO LTD

A method for identifying drought-resistant genes in potatoes using hyperspectral

The application provides a method for identifying potato drought-resistant genes using hyperspectral, and relates to the technical field of crop drought-resistant gene identification, and comprises the following steps: setting a drought group and a control group, synchronously acquiring plant canopy hyperspectral images and transcriptome data and establishing a correlation data set; extracting spectral features, screening drought response candidate genes; calculating the correlation coefficient of each candidate gene and the spectral features based on Spearman correlation analysis, and determining the primary gene set according to whether the average value of a plurality of positions after the absolute value is sorted exceeds a threshold value; constructing a random forest regression model with the spectral features as input and the expression amount of the primary gene as output, predicting the expression amount through a verification sample, and screening target drought-resistant genes according to the coefficient of determination and the prediction error; constructing a target gene overexpression plant, measuring the relative change rate of physiological indexes and the change multiple of gene expression amount under drought, calculating a comprehensive function verification index, and determining the gene as a drought-resistant gene if the index exceeds a threshold value.
Owner:INNER MONGOLIA AUTONOMOUS REGION ACAD OF AGRI & ANIMAL HUSBANDRY SCI

A method for biosynthesis of ginsenosides by using tobacco BY-2 cells as a chassis

The application discloses a method for biosynthesizing ginsenoside by using tobacco BY-2 cells as a chassis, and belongs to the technical field of bioengineering. The method comprises the following steps: firstly, a recombinant expression vector containing a key gene set of a ginsenoside synthesis pathway is constructed, wherein the gene set comprises tHMGR, SE, SS and other genes derived from Panax ginseng and Pn1-31 and Pn3-31 genes derived from Panax notoginseng; secondly, the recombinant vector is introduced into tobacco BY-2 cells, and a pure positive cell line is obtained through solid culture medium screening; finally, the positive cell line is cultured in liquid or solid culture medium to obtain ginsenoside Rh2 and / or Rg3. The application successfully reconfigures a rare ginsenoside synthesis pathway by taking advantage of the fast growth and stable culture of tobacco BY-2 cells, realizes efficient heterologous synthesis of the rare ginsenoside, and provides a repeatable technical scheme for industrial production of the rare ginsenoside.
Owner:ZHEJIANG FINDYOU BIOTECHNOLOGY CO LTD

Early gastric cancer lymph node metastasis risk prediction method and system, application and medium

The invention relates to the technical field of methylation detection site detection, and particularly provides an early gastric cancer lymph node metastasis risk prediction method, system, application and medium, and the method comprises the following steps: obtaining a gastric cancer public data set containing a DNA methylation chip data set and an RNA sequencing data set, and carrying out sample screening, quality control and grouping processing to obtain eight quality control grouping samples; carrying out methylation and RNA difference analysis on the quality control grouped samples to obtain a related gene set of differential methylation sites and differential methylation regions and an RNA differential expression gene set; a gene set of differential methylation sites and an RNA differential expression gene set are integrated and screened to obtain eight target genes. The system comprises a sample acquisition module, a gene analysis module and a gene screening module. Target genes are analyzed and screened on the basis of database biological information, and methylation detection sites for histopathological specimens are screened in combination with lymph node metastasis positive and negative early gastric cancer histological sample verification.
Owner:CHANGZHOU NO 2 PEOPLES HOSPITAL