30 results about "Gene interaction network" patented technology

The invention relates to a method and a system for constructing a dynamic gene regulation network, computer equipment, a computer readable storage medium, a computer program product and a computer program. The method comprises the following steps: constructing a plurality of single cell quasi-time sequence differentiation trajectories based on single cell transcriptome data of a plurality of single cells; determining a dynamic change gene in a target quasi-timing sequence differentiation trajectory based on the plurality of single cell quasi-timing sequence differentiation trajectories; constructing an initial static gene interaction network based on the dynamic change gene; and performing inspection based on the initial static gene interaction network to obtain the dynamic gene regulation network. According to the method, key gene regulation mechanisms corresponding to different differentiation stages of the cells can be rapidly determined, and the real dynamic change condition of the gene regulation relationship in the biological process is reflected.

The invention discloses a breast cancer prognosis real-time evaluation system and method fusing a multi-modal image and a co-disease network, and relates to the technical field of breast cancer prognosis evaluation. According to the system, a comprehensive feature matrix fusing images, genes and clinical features is constructed by acquiring a mammary gland medical image, extracting focus features and combining gene expression information of a focus area and co-disease data of a patient, feature weighting is carried out based on an attention mechanism, and finally a prognosis risk score is output by utilizing a multi-layer perceptron model. And risk grading and intervention suggestion generation are realized. According to the system, a co-disease network and a gene interaction network are introduced for modeling, relevance expression among multi-source information is enhanced, and pathological features and systematic health status of patients can be reflected comprehensively. The intelligent level of prognosis evaluation can be improved, and good clinical popularization value is achieved.

The invention discloses a cancer driver gene prediction method and system based on a graph neural network, and the method comprises the steps: obtaining interaction data of M proteins; for each kind of protein interaction data, coding a relationship between proteins into a gene-gene interaction relationship, and finally obtaining M gene-gene interaction networks; configuring new nodes and new edges for the M genes and gene interaction networks respectively to obtain M heterogeneous networks; the new nodes are cancer-related multi-omics data, and the new edges are connection edges between the new nodes and original gene nodes; and inputting each heterogeneous network into a trained cancer driving gene prediction model to obtain a prediction result of whether each gene is a cancer driving gene or not.

The invention discloses a genomics-based biomarker screening method and system, and relates to the technical field of biological detection.The method comprises the steps that biomarker expression data related to significant genes are determined according to transcriptome sequencing data of a biological sample of a cancer disease, the posterior distribution of the biomarker associated with the cancer disease is estimated through a logistic regression model; determining significant interaction genes according to the posterior distribution and the interaction network between the genes; and based on the significant interaction genes, screening to obtain a biomarker list related to cancer diseases. According to the application, the posterior distribution and significant interaction genes are screened through the transcriptome sequencing data of the biological sample of the cancer disease, so that the situation of missing detection caused by low biomarker specificity in the traditional biomarker screening process is avoided, and a biomarker list highly related to the cancer disease can be obtained; and the sensitivity of the biomarker screening process is improved.

The invention relates to the technical field of biological information, and provides a whole genome selection method, device and equipment of a graph neural network and a storage medium, and the whole genome selection method of the graph neural network comprises the following steps: mapping single nucleotide polymorphism (SNP) to a gene level, and converting the SNP into a gene embedding vector; constructing a gene interaction network based on preset multi-source biological priori knowledge; inputting the target character into a graph neural network model to obtain a predicted value of the target character output by the graph neural network model; wherein the graph neural network model is determined based on a gene embedding vector and a gene interaction network. According to the method, the SNP is mapped to the gene level, and the gene interaction network is combined, so that the prediction result has clear biological significance; and the gene interaction network is constructed based on the preset multi-source biological priori knowledge, so that interaction information between genes can be fully utilized, and the accuracy of target character prediction is improved.

The invention discloses a multi-layer heterogeneous network unicellular organism network inference method based on meta-path enhancement, which mainly comprises a gene regulation knowledge base enhanced multi-layer heterogeneous network construction module for integrating an external gene interaction network and multiple omics data such as scRNA-seq, scATAC-seq, ST and the like; constructing a single-cell multi-omics multilayer heterogeneous network containing cell-cell, cell-gene and gene-gene relationships, and fusing spatial constraints to consider cell positions and tissue structures; and the feature enhancement module based on the meta-path explores complex semantics of the network by designing a multi-hop meta-path mode, designs an adaptive multi-view learning framework and a multi-round enhancement mechanism, and optimizes feature representation by using cell-gene interaction and cross-modal attention fusion. The unicellular biological network can be effectively deduced, the deduction accuracy and biological interpretation are remarkably improved, the method plays an important role in understanding the cell biological process, developing and treating diseases and the like, has good expandability, and can further integrate multi-modal omics data such as proteomics and metabonomics.

The invention discloses a lung cancer drug resistance prediction method based on user feature analysis, and relates to the technical field of biological information processing, and the method comprises the steps: calling a biological gene pool, analyzing and mining a gene interaction network based on gene variation statistics of targeted drugs, supervising and training a drug resistance detector based on a self-attention mechanism, receiving user inspection data, and predicting the drug resistance of the lung cancer; and controlling a sequencer to carry out gene sequencing detection, determining a user gene sequence, transmitting the user gene sequence to a drug resistance detector, and determining a variation trend of a targeted fragment so as to analyze drug resistance prediction data under a time sequence. The method and the device are used for solving the technical problem that the accuracy of a prediction effect is limited due to insufficient depth and comprehensiveness of drug resistance analysis in the prior art. Drug resistance analysis is carried out based on variation prediction of the target gene, and the accuracy of drug resistance prediction can be effectively improved.

The present invention discloses a constrained multi-objective optimization method for detecting drug targets in individual cancer patients, comprising: constructing a personalized gene interaction network (PGIN) from the genomic data of the individual patient; forming a structural network control model based on multi-objective optimization; and using a constrained multi-objective evolutionary algorithm to search for a personalized drug target set, i.e., a driver gene set. The present invention can effectively identify drug targets in individual cancer patients, explore cancer heterogeneity, and provide a new perspective for understanding tumor heterogeneity in precision medicine.

The invention is suitable for the technical field of bioinformatics, and provides a gene interaction network analysis system and method based on symbology dynamics. The method comprises the steps of original gene data preprocessing, dynamic gene interaction network construction, network dynamic state symbol coding, symbol sequence feature analysis, analysis strategy dynamic adjustment, key information identification and result output. The system comprises corresponding function modules. According to the method, a symbolic dynamics theory and gene interaction network analysis are fused, a gene network dynamic process is converted into a symbol sequence through an exclusive symbol coding algorithm, network dynamic characteristics are extracted by means of methods such as symbol entropy calculation and symbol pattern recognition, and meanwhile, a dynamic adjustment analysis strategy is introduced; according to the method, a dynamic self-adaptive analysis system is constructed, dynamic changes of gene expression and regulation relationships are accurately described, the recognition accuracy of key interaction relationships, key nodes and key paths of a complex network is improved, and the method has important theoretical value and practical application prospects.

The application belongs to the technical field of picture processing, and particularly relates to a picture generation method based on mutation data, a generation system and a cancer metastasis prediction method. Step one: constructing a pathway image by using the functional similarity of pathways on a gene interaction network; step two: constructing a patient characteristic image; the prediction method further comprises: training a prediction model by using the constructed patient characteristic image, and predicting the metastasis of mutation data by using the trained prediction model. The application aims to solve the problems of lacking high-performance generation of patient characteristic pictures based on single nucleotide variation and the technical problems of cancer metastasis prediction and determination.

A method for simultaneously deducing single-cell pseudo time, velocity field and gene interaction comprises the following steps: preprocessing a single-cell RNA sequencing data set of cell development with multiple branches, clustering different cell types, constructing a piecewise linear model, optimizing the piecewise linear model by adopting an expectation maximization algorithm, and calculating the single-cell pseudo time, velocity field and gene interaction. Deduced pseudo time of each cell, a gene interaction matrix of the dynamic network and single cell velocity field visualization on a pseudo time chart are obtained. According to the method, a segmented ordinary differential equation model is introduced to reconstruct an RNA velocity field and pseudo time of a cell and an interaction network between genes. By iteratively optimizing a connection matrix between genes and pseudo time of the cells, the prediction precision of dynamic change of the cells can be remarkably improved, cell state transition can be accurately deduced, and a key gene regulation and control relationship can be accurately detected.

The invention discloses a multi-gene interaction network prediction method and system based on a graph neural network. The method comprises the following steps: S1, acquiring multi-source biological data; s2, carrying out pretreatment; s3, constructing a gene map; s4, fusing the edge weight matrix and the node feature matrix in the gene map through a dynamic attention mechanism, and outputting a refined feature set; s5, acquiring an optimal hyper-parameter set by using a Bayesian optimization algorithm; s6, based on the gene map and the optimal hyper-parameter set, training the attention enhancement map neural network to obtain a multi-gene interaction network prediction model; and S7, predicting the interaction relationship of the unknown gene pair by using the multi-gene interaction network prediction model, and outputting a result. According to the method, the gene map is constructed through multi-source data fusion, the gene association information is enriched, the multi-head attention map neural network is introduced to automatically learn the interaction weight, the hyper-parameters are dynamically adjusted in combination with Bayesian optimization, and the prediction accuracy and model universality of the multi-gene interaction network are improved.

The invention discloses a multi-omics cancer sample representation method based on graph representation and a related device. The representation method comprises the following steps: acquiring gene common library data; processing the gene public library data to obtain gene expression data and methylation data of which the variance of the cancer sample is greater than a threshold value; processing the gene expression data of which the variance of the cancer sample is greater than a threshold value and the methylation data to obtain multi-omics data of the cancer sample, and taking an intersection of the multi-omics data of the cancer sample to obtain a common gene; obtaining a gene interaction network of the corresponding gene through a protein interaction network database on the basis of the common gene, filtering out part of scattered points in the gene interaction network, and integrating to obtain a sample gene interaction network skeleton; and integrating the multi-omics data of the cancer sample and the sample gene interaction network skeleton representation by adopting a sample graph representation algorithm. According to the method, multiple omics data are processed to obtain omics data corresponding to genes highly related to cancer occurrence, so that the influence of experimental deviation in measurement and sequencing data on subsequent conclusions is reduced.

The present invention provides a cancer co-driving module identification system based on single-cell data, comprising: a data preprocessing module: integrating copy number variation data and single nucleotide polymorphism data into mutation data, performing gene alignment and preliminary screening on multi-omics data to obtain available multi-omics data, where the multi-omics data at least includes single-cell gene expression data; a functional association network construction module: constructing a functional association network based on single-cell gene expression data and a gene interaction network; a functional cluster acquisition module: applying overlapping Markov clustering to the functional association network to obtain multiple functional clusters; a driving module identification module: based on a module weight evaluation function, using greedy search to identify driving modules on the functional clusters; a co-driving module identification module: according to a driving module distance function, determining the identified driving modules as co-driving modules; the present invention realizes the efficient and accurate identification of co-driving modules.

This invention provides a multi-to-multi drug screening method for CRISPRa / i GPCR libraries based on a three-dimensional spatial hybrid screening model and its applications, belonging to the field of biomedical technology. The method includes the following steps: Step (1): Constructing a screening cell pool; Step (2): Classifying the drugs to be screened; Step (3): Constructing a drug hybrid screening model; Step (4): Grouping drugs according to mutually perpendicular X, Y, and Z planes, with drugs in each plane mixed to form independent pools; Step (5): Processing each pool into a cell pool; Step (6): Detecting and analyzing the changes in sgRNA abundance in each pool; Step (7): Decoding to determine the drug-GPCR interaction pairs. This invention offers higher screening throughput, realizes a multi-target, multi-drug screening mode, reduces costs and time, and enables large-scale research on drug-gene interaction networks, which is of great significance for drug research and development.

The invention discloses a queen bee breeding value evaluation and core population selection method based on multi-omics data, and relates to the technical field of bee genetic breeding and multi-omics data application, and the method comprises the steps: obtaining candidate queen bee genome, intestinal microbiome and host transcriptome data; analyzing data and screening disease-resistant related core microbial markers, immune genes and bacterium-gene interaction network characteristics; by taking the characteristics as input, constructing a machine learning model to calculate a disease-resistant genome-microbiome combined breeding value; combining the breeding value, a core group genetic coefficient and an intestinal flora diversity index to construct a comprehensive selection index; according to the method, accurate evaluation of disease-resistant breeding values is achieved through multi-omics fusion and machine learning, genetic relationship and flora diversity optimization selection are combined, the disease resistance and genetic diversity of the core populations are improved, and a scientific basis is provided for queen bee breeding.

The invention discloses a method for analyzing treatment of chronic pelvic inflammation by motherwort based on network pharmacology, and relates to the technical field of medical treatment, which comprises the following steps: firstly, screening active components of motherwort from TCMSP and BATMAN-TCM databases through multi-dimensional data mining and interaction network modeling, and then predicting potential action targets of the active components by using SwisTargetPredictions and CTD databases; the method comprises the following steps: searching a target gene related to the CPID by utilizing two databases, namely a GeneCards database and an OMIM database; the method comprises the following steps: identifying common genes of active components such as quercetin of motherwort and a CPID target gene through a motherwort-target gene-CPID interaction network, and constructing a regulatory network by using Cytoscape software; according to the method, protein interaction network analysis is carried out by adopting an STRING database, in-depth analysis is carried out on network topology characteristics by applying Cytoscape, and function enrichment analysis (GO and KEGG) is carried out on key genes by adopting a cluster Profiler packet of an R language. A research result shows that the motherwort regulates and controls a plurality of key biological pathways and molecular processes through a multi-component and multi-target synergistic effect, so that the treatment effect of the motherwort on CPID is exerted.

The present application discloses a genomics-based biomarker screening method and system, which relates to the field of biological detection technology. The method comprises: determining biomarker expression data associated with significant genes based on transcriptome sequencing data of cancer disease biological samples, and estimating the posterior distribution of the association between biomarkers and cancer diseases through a logistic regression model; determining significant interacting genes based on the posterior distribution and the gene interaction network; and screening to obtain a list of biomarkers associated with cancer diseases based on the significant interacting genes. Since the present application screens the posterior distribution and significant interacting genes through transcriptome sequencing data of cancer disease biological samples, it avoids the situation in which missed detections are caused by low biomarker specificity in the traditional biomarker screening process, thereby obtaining a list of biomarkers with high correlation with cancer diseases, and improving the sensitivity of the biomarker screening process.

The present invention discloses a compound combination screening method based on key genes for resisting parasitic infections, comprising: 1. After preprocessing biological data, a single-layer differential interaction network is constructed for each individual infected by parasites, and a multi-layer gene interaction network is constructed by connecting the corresponding gene nodes of multiple single-layer networks to achieve the fusion of multiple networks, and then the PageRank algorithm of the multi-layer network is used to calculate the score of the gene in each layer of the network, and the average score of the corresponding same gene in all layers is used to sort and identify the key gene; 2. Based on the key gene and the known FDA-approved compounds and the target gene set of each compound, a multi-objective optimization function model is designed, and a multi-objective optimization algorithm is used to obtain a better compound combination. The present invention can improve the time efficiency of screening the compound combination for resisting parasitic infections and screen out a better compound combination.

The invention discloses an intelligent autumn pear whole genome association analysis system based on deep learning, and relates to the technical field of gene deep learning, which comprises the following steps: collecting genotype data and phenotype data of autumn pears, obtaining a standardized data set through preprocessing, converting the standardized data set into a matrix form by adopting an image coding method, and carrying out correlation analysis on the whole genome of the autumn pears; extracting spatial features, and generating image data; analyzing the interaction among the multiple-effect gene identification data by adopting a graph convolutional network, obtaining gene interaction characteristics, identifying gene clusters participating in the same biological process, and generating a gene interaction network; and combining the gene interaction network with a deep convolutional neural network, analyzing the relationship between the genotype data and the phenotype data, obtaining deep feature data, identifying the gene locus of the pyrus ussuriensis, and generating a key gene locus analysis scheme. According to the method, the accuracy of genome correlation analysis is effectively improved, and important support is provided for gene research and accurate breeding of pyrus ussuriensis.

The invention relates to the technical field of environmental microbial toxin detection, in particular to a qPCR technology-based algal toxin production gene detection analysis method and system, and the method comprises the following steps: generating an original amplification curve; outputting an effective amplification curve after the PCR inhibition effect is eliminated; obtaining an algae toxin-producing gene database, performing dynamic baseline correction on the effective amplification curve, and outputting a baseline correction curve; calculating a second derivative of the baseline correction curve and positioning a global maximum point; based on the global maximum value point, determining a self-adaptive threshold value, and calculating a Ct value representing the expression level of the target gene; obtaining a toxin expression profile database, and constructing a gene interaction network based on the Ct value; the gene interaction network is analyzed, and the toxin production potential state is judged; and integrating the effective amplification curve, the Ct value, the gene interaction network and the toxin production potential state to generate a detection report. According to the method, the accuracy and the reliability of detecting the toxin-producing genes of the algae are remarkably improved.

The application provides a transcription factor target gene relationship prediction method, system, device and medium, and the method comprises the following steps: obtaining DNA sequences of transcription factors and DNA sequences of target genes of a to-be-predicted species and encoding to obtain encoded sequences; obtaining protein and genetic interaction network data and transcription factor target gene interaction network data of the to-be-predicted species; constructing a graph neural network model based on the encoded sequences, the protein and genetic interaction network data and the transcription factor target gene interaction network data, and performing model training to obtain a trained graph neural network model; and predicting unknown transcription factor target gene interaction relationships of the to-be-predicted species by using the trained graph neural network model. The application can avoid the problems of a large number of missing values of gene expression data and inaccurate binding site prediction; meanwhile, large-scale transcription factor-target gene potential relationship prediction can be realized according to the topological structure of an existing gene regulation network.

The application discloses a kind of multi-omics cancer sample representation methods based on graph representation and related devices, representation method includes: obtaining gene public library data;Gene public library data is handled, and the gene expression data and methylation data of the variance of cancer sample is greater than threshold value are obtained;After the gene expression data and methylation data of the variance of cancer sample is greater than threshold value are handled, the multi-omics data of cancer sample is obtained, the intersection of the multi-omics data of cancer sample is obtained, and the common gene is obtained;Based on common gene, the gene interaction network of corresponding gene is obtained through protein interaction network database, after filtering out part of scatter point in gene interaction network and integration, the sample gene interaction network skeleton is obtained;The multi-omics data of cancer sample and sample gene interaction network skeleton representation are integrated using sample graph representation algorithm.The application processes multi-omics data, obtains the omics data corresponding to the gene highly related to cancer occurrence, so as to reduce the influence of experimental bias in measurement and sequencing data on subsequent conclusion.

A kind of anti-cancer cell sensitivity prediction method, system, equipment and medium of fusion gene network relationship, method includes: the vector of the expression amount of each gene of cell line is as the original gene expression feature of cell line, compressed low-dimensional hidden vector is used as the gene expression feature of cell line by using self-encoder, graph self-encoding is carried out to gene interaction network to obtain gene interaction feature, gene network feature is calculated according to gene expression feature and gene interaction feature, the feature of each atom in drug compound molecule is obtained by establishing drug compound molecular graph, and the predicted anti-cancer cell sensitivity is obtained according to EIGA model;System, equipment and medium are used to realize a kind of anti-cancer cell sensitivity prediction method of fusion gene network relationship;The present application fully considers the interaction relationship between genes and the topological structure in compound molecule by designing new algorithm, realizes the anti-cancer cell sensitivity prediction on cell line and single cell level.

The invention belongs to the technical field of biological medicine, and relates to a gastric cancer biomarker mining method and system. The method comprises the following steps: acquiring data; preprocessing the data; generating a gene interaction network; performing data difference analysis; performing function enrichment analysis; analyzing a survival prognosis model gene; carrying out GSEA enrichment analysis; carrying out progression-free lifetime analysis; a Nomogram model is constructed; analyzing the causal relationship between the gastric cancer biomarker and the gastric cancer; analyzing the causal relationship between protease and gastric cancer; and analyzing the causal relationship between the gastric cancer biomarker and the protease. According to the invention, the gastric cancer mechanism is explored by combining a bioinformatics method and a Mendel randomization method, and the gastric cancer biomarker indirectly affects the occurrence of gastric cancer through mediated protease, so that the mining of the gastric cancer biomarker is realized.

The invention provides a method and system for analyzing dysregulated biological pathways associated with states of interest to identify risks and molecular targets for personalized treatment. The method employs a two-layer machine learning model (MLM) to assign dysregulated pathway (DP) scores to biological pathways derived from both whole-genome co-expression network analysis and differential gene expression analysis. In the first layer, classifiers are used to predict states based on the identified pathways. In the second layer, a stacking classifier integrates these predictions to compute the final state. Each pathway is weighted according to its contribution to the state of interest, and pathway scores are normalized to reflect their relative significance. The method incorporates the Shapley Additive Explanations (SHAP) technique to enhance model interpretability. This enables the identification of key genes and molecular targets. This method and system are patient-independent, offering a framework for precision medicine across a wide range of conditions.

The application belongs to the technical field of biometric recognition, and relates to a key pathogenic factor screening method based on deep embedding and gene network constraint. The method first acquires a gene expression matrix; a gene interaction network corresponding to the gene expression matrix is constructed to generate a sparse adjacency matrix and a sparse mask matrix; a graph variational autoencoder model with gene network constraint is constructed, the input of the model is the gene expression matrix, the sparse mask matrix M is used in the form of element-level multiplication to limit the weight connection of the encoder, the decoder reconstructs the input gene expression matrix according to the latent structure characteristics, and a multi-task prediction module at the output end predicts the infection stage probability distribution and pathogen load through parallel classification branches and regression branches; the constructed model is trained; feature attribution analysis is performed on the input genes according to the task output of the model, the importance scores of the genes are calculated, and a key gene candidate set is generated. The method significantly improves the biological rationality and stability of the screening result.

The application discloses a high-perturbation gene priority ranking system, which comprises a gene interaction network, a hub gene identification module, a knockout perturbation initialization module and a perturbation propagation network.

The invention discloses an individualized coding and non-coding cancer pathogenic gene identification method based on gene interaction network node centrality. The method comprises the following steps: constructing an individualized lncRNA-TF-mRNA gene interaction network for a patient through expression data of coding genes TF and mRNA of the patient and expression data of a non-coding gene lncRNA, and centrally evaluating a gene node on the established individualized lncRNA-TF-mRNA gene interaction network in combination with the gene interaction network of the gene node. Coding and non-coding cancer pathogenic genes of a patient are ranked to identify cancer pathogenic genes. The method has the beneficial effects that by implementing the method, the identification accuracy of individualized coding and non-coding cancer pathogenic genes is effectively improved.

The invention belongs to the technical field of biological feature recognition, and relates to a key pathogenic factor screening method based on deep embedding and gene network constraint, and the method comprises the steps: firstly obtaining a gene expression matrix; constructing a gene interaction network corresponding to the gene expression matrix, and generating a sparse adjacent matrix and a sparse mask matrix; a graph variational auto-encoder model constrained by a gene network is constructed, the input of the model is a gene expression matrix, an encoder adopts a sparse mask matrix M to limit weight connection in the form of element-level multiplication, and a decoder reconstructs the input gene expression matrix according to potential structural features. A multi-task prediction module at an output end predicts probability distribution and pathogen load of an infection stage through parallel classification branches and regression branches; the constructed model is trained; feature attribution analysis is conducted on input genes according to task output of the model, importance scores of all the genes are calculated, a key gene candidate set is generated, and the biological rationality and stability of screening results are remarkably improved through the method.