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54 results about "Protein Interaction Networks" patented technology

A method for analyzing the co-mechanism of hepatotoxicity and nephrotoxicity of non-steroidal anti-inflammatory drugs

The application provides a method for analyzing the synergistic mechanism of hepatotoxicity and nephrotoxicity of non-steroidal anti-inflammatory drugs. The method comprises the following steps: preliminary toxicity prediction of NSAIDs and collection of toxicity target points, collection of liver and kidney disease target points, then cross and screening of the target points to obtain core target points and common core target points of NSAIDs induced liver and kidney diseases, and then constructing a protein interaction network of the common core target points; enrichment analysis of the common core target points to obtain the common action pathway of NSAIDs induced liver and kidney diseases; finally, further screening of the common core target points to obtain the key target points of NSAIDs induced liver and kidney diseases, and verification by using molecular docking technology. Compared with the traditional method, the advantages of the method are: first, the method does not depend on large-scale patient clinical data and a large number of animal or cell experiments, avoiding the ethical controversy in animal experiments and human experiments; second, the method can identify the potential cross-pathway and synergistic toxicity mechanism when a compound triggers multiple diseases, which is helpful for more comprehensive evaluation of the toxicity risk of NSAIDs.
Owner:GUANGDONG UNIV OF TECH

Protein network overall effect-based drug optimization method and system

The embodiment of the invention provides a drug optimization method and system based on the overall effect of a protein network. The method comprises the following steps: constructing a protein interaction network related to a target disease, and dividing each protein target into a risk protein set and a protection protein set; respectively calculating first binding affinity data of the candidate drugs and each protein target in the risk protein set, and generating a first network comprehensive score based on the first binding affinity data; respectively calculating second binding affinity data of the candidate drugs and each protein target in the protection protein set, and generating a second network comprehensive score based on the second binding affinity data; calculating network confrontation scores of the candidate drugs according to the first network comprehensive score and the second network comprehensive score; and determining whether the candidate drug is a preferred drug based on the network adversarial score. The method can overcome the defect that a single-target drug is insufficient in curative effect due to a network compensation effect, so that safer and more effective candidate drugs are screened out.
Owner:SHANGHAI PUDONG HOSPITAL +1

Traditional Chinese medicine efficacy evaluation method and device based on node weighted network, equipment and storage medium

ActiveCN121545787BImprove biological explanatory powerbiologically reasonableChemical property predictionMolecular designMedicinal herbsDisease
The disclosure provides a traditional Chinese medicine efficacy evaluation method and device based on a node-weighted network, equipment and a storage medium. The method determines target disease protein targets and corresponding target weights based on the comprehensive scoring results of candidate disease protein targets by a public database and a large language model. When determining the protein targets of medicinal materials and the corresponding protein target weights of medicinal materials, the prescription ratio, chemical component information, and the interaction probability between the chemical components and the protein targets of each medicinal material in the traditional Chinese medicine prescription to be evaluated are comprehensively considered. The target disease protein targets and the corresponding disease protein target weights, as well as the protein targets of medicinal materials and the corresponding protein target weights of medicinal materials, are added to a pre-constructed protein interaction network. The obtained node-weighted network focuses on the real pharmacological basis, effectively improves the network biological interpretation, and the multi-dimensional network index determined accordingly is used to evaluate the regulation effect of the traditional Chinese medicine prescription to be evaluated on the target disease, which is more accurate.
Owner:INNOVATION CENTER OF YANGTZE RIVER DELTA ZHEJIANG UNIVERSITY

Method for drawing human full-coverage protein interaction network based on digital PCR next-generation sequencing

The invention discloses a method for drawing a human full-coverage protein interaction network based on digital PCR next-generation sequencing. After the advanced pedestrian 293T cell line obtains mRNA, a modified random primer or an oligo-dT primer is adopted to obtain a cDNA library; carrying out homogenization treatment on the human cDNA library; the method comprises the following steps: transforming plasmids of a BACTH bacteria double-hybrid system to obtain transformed plasmids; carrying out homologous recombination on the transformed plasmids of the sample library and the double-impurity system, and introducing into escherichia coli for screening to obtain positive PPI clones of the library with interaction; and carrying out digital PCR-based next-generation sequencing on the screened clones to draw the human full-coverage protein interaction network. The method is suitable for performing high-throughput screening after thousands of positive PPI combinatorial clones are obtained by'library-to-library 'bacteria or yeast double hybrids, identifying the same cell bar code cDNA combinatorial pairs, and realizing PPI network identification in different species, among species and in hybridization technology system extensive scenes.
Owner:LIANGZHU LAB

Molecular docking analysis method of core target based on RCSB database

This invention discloses a molecular docking analysis method for obtaining core targets based on the RCSB database, comprising: screening drug-disease-immunity intersection targets through multiple databases; screening core targets through protein interaction network analysis and multi-topology algorithms; obtaining core target structure files from the RCSB database and downloading active ingredient structure files from the PubChem database; performing molecular docking through the CB-DOCK2 database; screening effective binding pairs using binding energy as an indicator and visualizing the results; and finally outputting the results through functional annotation and pathway enrichment analysis. This method improves the accuracy of core target screening and the reliability of molecular docking through multi-database integration, multi-algorithm collaboration, and multi-dimensional evaluation, forming a complete technical chain and providing efficient technical support for the analysis of the mechanisms of action of traditional Chinese medicine compound prescriptions.
Owner:INNER MONGOLIA UNIV FOR THE NATITIES

Cancer driver gene interpretable identification method based on trust calibration and prototype learning

ActiveCN122177237BAlgorithmMessage delivery
The application relates to a cancer driver gene explainable identification method based on trust calibration and prototype learning, and relates to the technical field of biological information identification. A gene graph is constructed by fusing a protein interaction network and gene multi-omics characteristics, and part of nodes are labeled. Label-aware message passing is performed through a trust calibration encoder, the neighborhood is split into a labeled part and a non-labeled part for independent calibration, and node embedding is adaptively fused. An angle margin prototype classifier is used to construct a class prototype on a hypersphere, the decision boundary is expanded, and a prediction result is output. A pivot node self-supervised regularizer is introduced, center nodes are screened from labeled driver genes, positive constraints are applied to neighbor non-labeled nodes, negative penalties are applied to non-neighbors, and a supervised boundary is maintained when non-labeled data is used. Finally, a structured explanation module is used to reuse the internal evidence of the model, a verifiable explanation is provided for prediction, and the unification of high precision and credible explanation is realized.
Owner:XIAMEN UNIV OF TECH

Cross-linking agent with mass spectrum fragmentable trehalose disaccharide as skeleton structure and preparation and application thereof

PendingCN121824643AEsterified saccharide compoundsSugar derivativesHydroxylamineProtein protein interaction network
The invention relates to a novel chemical cross-linking agent with mass spectrum fragmentable trehalose disaccharide as a skeleton structure and a preparation method thereof. The cross-linking agent disclosed by the invention has the following characteristics: 1) trehalose disaccharide is used as a skeleton structure, so that the cross-linking agent has excellent biocompatibility; 2) the trehalose skeleton has a pair of symmetrical mass spectrum fragmentable glucosidic bonds, so that a cross-linked peptide fragment can be simplified into a conventional peptide fragment modified by a cross-linking agent fragment; 3) the enrichment of the cross-linked peptide fragment can be realized by the trehalose skeleton under the condition of not adding an enrichment handle; and 4) active groups of the cross-linking agent comprise but not limited to a plurality of reactive groups such as succinamide ester, diaziridine, phenylsulfonyl fluoride, hydrazide group, amino group, hydroxylamine group and the like, and chemical cross-linking of a plurality of amino acids except lysine is realized. The trehalose cross-linking agent disclosed by the invention is applied to the field of proteomics, and provides technical support for realizing large-scale analysis of a protein complex in a complex sample, spatial structure analysis of protein and a protein-protein interaction network.
Owner:DALIAN INSTITUTE OF CHEMICAL PHYSICS CHINESE ACADEMY OF SCIENCES

A method of identifying a cell subpopulation associated with a disease phenotype

ActiveCN116959562BData visualisationProteomicsDisease phenotypeDisease
A method for identifying cell subpopulations associated with disease phenotypes, belonging to the biomedical field. To identify cell subpopulations associated with disease phenotypes, this invention collects single-cell RNA sequencing data of the disease to obtain a single-cell expression matrix, collects the bulk expression matrix of the disease and corresponding phenotypic tags, and downloads human protein-protein interaction data to construct a protein-protein interaction network; extracts gene signature features of cells and samples and maps them to the protein-protein interaction network to form corresponding cell modules and sample modules; calculates the distance between each cell module and each sample module, and determines a set of multiple sample modules as the sample module set of the disease phenotype; calculates the distance between cell modules and the sample module set of the disease phenotype; creates a background distance distribution to evaluate the statistical significance of the distance between cell modules and the sample module set of the disease phenotype, and identifies cells whose distance to the sample module set of the disease phenotype is significantly smaller than the background distance distribution.
Owner:NORTHEAST FORESTRY UNIV

Network medicine framework for identifying drug repurposing opportunities

ActiveUS12670969B2Protein protein interaction networkGraph neural networks
Methods and systems for generating drug repurposing predictions for a disease caused by a pathogen, such as a novel pathogen, are provided. A multi-modal system includes a protein-protein interaction network (PPI), a graph neural network (GNN), a diffusion module, a proximity module, and an aggregation module. The GNN is configured to predict new edges between candidate drug nodes and disease nodes in an embedded representation of the PPI to produce a decoded embedding space. The diffusion module is configured to determine a proximity distance for pairs of nodes in the PPI, and the proximity module is configured to determine a proximity distance for pairs of nodes in the PPI, each pair comprising a pathogen-protein node and a drug-protein node. A ranked list of candidate drugs predicted to be effective in treatment of the disease based on candidate drug lists generated by the other modules is generated by the aggregation module.
Owner:NORTHEASTERN UNIV (US) +3

A method for predicting metabolic state and metabolic feature subtype of cancer cells

The application discloses a method for predicting different metabolic states of cells in cancer and metabolic characteristic subtypes of the cells based on a metabolite-protein interaction network, and the method comprises the following steps: (1) identifying the classification and metabolic state of the cells: preprocessing data, filtering low-quality cells; performing twice principal component analysis according to key genes; performing twice dimension reduction clustering on the cells respectively; (2) predicting metabolic characteristic subtypes of a queue according to the proportion of different metabolic states of cells in the sample. The method can identify the metabolic state of the cells and metabolic subtypes, and provides a new perspective for cancer research.
Owner:DALIAN INSTITUTE OF CHEMICAL PHYSICS CHINESE ACADEMY OF SCIENCES +1

Traditional Chinese medicine intelligent matching system based on network targeting comprehensive index and screening method thereof

A traditional Chinese medicine intelligent screening method based on network targeting comprehensive indexes belongs to the technical field of traditional Chinese medicine intelligent screening. The method comprises the following steps: constructing a target set A and a protein interaction network database corresponding to each traditional Chinese medicine; constructing a disease core gene set B based on a protein interaction network; calculating a network targeting comprehensive index based on the target point set A and the disease core gene set B; calculating the network targeting comprehensive index of each traditional Chinese medicine and then performing ascending sorting, wherein the smaller the network targeting comprehensive index is, the stronger the network targeting relevance between the traditional Chinese medicine and the disease is; and matching the traditional Chinese medicines according to the obtained ascending order, and generating a structured and explainable final recommendation report. According to the method, the disease-related gene identification accuracy is improved, the biological interpretation of the result is enhanced, the standardized processing of integrating multi-source data into intelligent recommendation is realized, and the urgent demand of efficient and accurate screening in modern research of traditional Chinese medicines is met.
Owner:HARBIN INST OF TECH +1

Method for analyzing action mechanism of external medicine for treating liver cancer ascites

The invention discloses an action mechanism analysis method of an external medicine for treating liver cancer ascites, and relates to the technical field of medicines. Comprising the following steps: screening active ingredients and related targets of a medicine through network pharmacology; predicting liver cancer ascites related disease targets; constructing an intersection target point network of active ingredient target points and disease target points, and performing protein interaction network analysis; carrying out GO function and KEGG pathway enrichment analysis on the intersection target spot; establishing a medicine, component, disease, target spot and pathway network; the binding activity of the core target and the active component is verified through molecular docking; establishing a liver cancer ascites model through animal experiments, and performing efficacy verification; network pharmacology and animal experiment data are integrated, and a drug action mechanism is analyzed. According to the invention, active ingredients, target spots and pathways of the medicine are rapidly screened through network pharmacology, so that the earlier-stage research period is greatly shortened; animal experiment design is standardized, samples can be processed in batches, and the method is suitable for high-throughput drug screening.
Owner:CHONGQING MEDICAL UNIVERSITY

Method and system for evaluating curative effect of traditional Chinese medicine prescription generated by large model based on network pharmacology

PendingCN121545781ADrug and medicationsProteomicsDiseaseProtein protein interaction network
The invention provides a network pharmacology-based large model generated traditional Chinese medicine prescription curative effect evaluation method and system, and the method comprises the steps: employing a machine learning model to generate candidate prescriptions, and obtaining all known active components of each traditional Chinese medicine in the prescriptions; predicting human body protein targets corresponding to the patient based on the known active components, and gathering all the human body protein targets to obtain a prescription target set P; obtaining human body protein targets related to the corresponding diseases, and gathering all the human body protein targets corresponding to the diseases to obtain a disease target set D; constructing a protein-protein interaction network; inputting the prescription target point set P and the disease target point set D into a protein-protein interaction network, and constructing a connected sub-network; calculating curative effect indexes of the connected sub-networks; and optimizing the prescription based on the curative effect index to complete the curative effect evaluation of the traditional Chinese medicine prescription. According to the method, calculation and experiments are closely combined, the blindness and the cost of experimental verification are remarkably reduced through a calculation priority strategy, and the research and development efficiency is improved.
Owner:CHONGQING UNIV OF POSTS & TELECOMM

Antibody specifically combined with arabidopsis thaliana blue light receptor cryptoflorin CRY1 and application thereof

PendingCN121537511AImmunoglobulins against plantsBiological testingOrganomercurial lyaseReceptor
The invention discloses an antibody specifically bound with arabidopsis thaliana blue light receptor cryptoflorin CRY1 and application thereof, and belongs to the technical field of biomedicine, the antibody has high specificity and high affinity when bound with arabidopsis thaliana CRY1 protein, and does not have cross reaction with arabidopsis thaliana CRY2, human CRY family protein and other species of photolyase / cryptoflorin, and the antibody can be used for detecting the photolyase / cryptoflorin of the arabidopsis thaliana blue light receptor cryptoflorin CRY1. The antibody can effectively solve the problems that an existing CRY1 detection method is poor in specificity, insufficient in sensitivity, unstable in result and the like, and a reliable tool is provided for expression dynamic tracking, subcellular localization and protein interaction network analysis of arabidopsis thaliana CRY1 protein.
Owner:JIANGSU DONGKANG BIOMEDICAL TECH CO LTD

A high-throughput general sample protein interaction screening method

The application discloses a high-throughput general sample protein interaction screening method. The method comprises the following steps: firstly, constructing a general sample open reading frame library, extracting mRNA of a target sample, and then obtaining a cDNA library by using a modified random primer or an oligo-dT primer; then, uniformly processing the general sample cDNA library; modifying plasmids of a double-hybrid system to obtain modified plasmids; homologously recombining the general sample library and the modified plasmids of the double-hybrid system, and introducing them into organisms to screen and obtain organisms with an interaction library; identifying single-cell PPI pairs of the screened organisms, and constructing a general sample protein interaction network. The application is suitable for screening and identifying the same Barcode cDNA combination pairs by using single-cell sequencing after obtaining tens of thousands of positive PPI combination clones by means of a "library-library" bacterial or yeast double-hybrid system, and realizing PPI network identification in different intra-species, inter-species and hybridization technology systems.
Owner:LIANGZHU LAB

Traditional Chinese medicine curative effect evaluation method and device based on node weighted network, equipment and storage medium

The invention provides a traditional Chinese medicine curative effect evaluation method and device based on a node weighted network, equipment and a storage medium. According to the method, a target disease protein target and a corresponding target weight are determined on the basis of a comprehensive scoring result of candidate disease protein targets by a public database and a large language model. When the medicinal material protein target and the corresponding medicinal material protein target weight are determined, the prescription proportion and the chemical component information of each medicinal material in the to-be-evaluated traditional Chinese medicine prescription and the interaction probability between the chemical component and the medicinal material target are comprehensively considered. A target disease protein target, a corresponding disease protein target weight, a medicinal material protein target and a corresponding medicinal material protein target weight are added to a pre-constructed protein-protein interaction network, and an obtained node weighted network focuses on a real pharmacological basis, so that the biological interpretation force of the network is effectively improved; the accuracy of evaluating the regulation effect of the to-be-evaluated traditional Chinese medicine prescription on the target disease by using the determined multi-dimensional network index is higher.
Owner:INNOVATION CENTER OF YANGTZE RIVER DELTA ZHEJIANG UNIVERSITY

Keratin related gene and application thereof in regulating and improving psoriasis

The invention relates to the technical field of biological medicine, and discloses a keratin related gene and application thereof in regulation and improvement of psoriasis, and the keratin related gene comprises KRT25, KRT28, KRT85 and KRTAP11-1. The invention also discloses application of the endocrine related gene in regulation and improvement of psoriasis, and the endocrine related gene is a CGA gene. By maintaining the expression level of the KRT25 gene, the KRT28 gene, the KRT85 gene, the KRTAP11-1 gene and / or the CGA gene, the psoriasis is relieved. The invention focuses on a dark green module, through GO / KEGG enrichment analysis, protein interaction network (PPI) construction and experimental verification, the molecular mechanism of OMT is further discussed, a network which takes keratin as a center and is related to endocrine (CGA gene) is clear as an effective node for psoriasis treatment, and a foundation is laid for discovery of a new target for psoriasis treatment.
Owner:NINGXIA MEDICAL UNIVERSITY GENERAL HOSPITAL

A method for drawing a human full-coverage protein interaction network based on digital PCR next-generation sequencing

The application discloses a method for drawing a human full-coverage protein interaction network based on digital PCR and second-generation sequencing. First, mRNA is obtained from a human 293T cell line, and then a cDNA library is obtained by using a modified random primer or an oligo-dT primer; then, the human cDNA library is uniformly processed; the plasmid of a BACTH bacterial double-hybrid system is modified to obtain a modified plasmid; the sample library and the modified plasmid of the double-hybrid system are homologously recombined and introduced into E. coli to screen positive PPI clones with interaction; and the screened clones are subjected to second-generation sequencing based on digital PCR to draw a human full-coverage protein interaction network. The application is suitable for high-throughput screening after obtaining tens of thousands of positive PPI combination clones by using a "library vs. library" bacterial or yeast double-hybrid system, and is suitable for identifying the same cell barcode cDNA combination to realize PPI network identification in different intra-species, inter-species and hybridization technology systems.
Owner:LIANGZHU LAB

Method for analyzing action mechanism of plasticizer acetyl tri-n-butyl citrate for inducing breast cancer based on network toxicology

The invention discloses a method for analyzing an action mechanism of a plasticizer acetyl tri-n-butyl citrate (ATBC) for inducing breast cancer based on network toxicology. The method comprises the following steps: firstly, integrating multiple databases to obtain and standardize ATBC targets, and identifying disease-related genes in combination with differential expression of TCGA data and weighted gene co-expression network analysis (WGCNA); overlapping target spots are obtained through intersection of the three, a protein interaction network is constructed, and function enrichment analysis is carried out. TCGA is used as a training set, GEO is used as a verification set, random forest and Lasso regression are combined to screen out core targets MAOA and ADRA2A, and a prognosis model is constructed. And finally verifying that the ATBC can be stably combined with the two target spots through molecular docking (the combination energy is 1t;-5.0 kcal / mol). According to the invention, a full-process scheme from target prediction, function analysis, machine learning screening to molecular docking verification is established, and a standardized normal form is provided for the study of the carcinogenic mechanism of environmental chemicals.
Owner:HUAIYIN INSTITUTE OF TECHNOLOGY

Traditional Chinese medicine effective component screening method based on chemical fingerprint spectrum and multi-omics conjoint analysis

The invention relates to a traditional Chinese medicine effective component screening method based on a chemical fingerprint spectrum and multi-omics combined analysis. The method comprises the following steps: preparing a semen cuscutae-fructus lycii medicine pair extract and establishing a UPLC-Q-TOF-MS / MS chemical fingerprint spectrum; detecting the levels of estradiol, luteinizing hormone, anti-mullerian hormone and follicle-stimulating hormone in the premature ovarian insufficiency animal model; screening characteristic components related to the drug effect through multivariate statistical analysis; performing transcriptome sequencing on the ovarian tissue, and combining GO / KEGG analysis to determine a key pathway; integrating database prediction targets and differential genes, screening hub genes and constructing a protein interaction network; and finally verifying the binding activity of the candidate component and the core target protein through molecular docking and molecular dynamics experiments. According to the invention, systematic screening and action mechanism analysis of drug effect related components are realized, and a new technical approach is provided for mass marker determination and estrogen simulating action research of the dodder-wolfberry drug pair.
Owner:HARBIN UNIV OF COMMERCE

Method for drawing mouse full-coverage protein interaction network through bacterial single cell transcriptome sequencing

The invention discloses a method for drawing a mouse full-coverage protein interaction network through bacterial single cell transcriptome sequencing. The method comprises the following steps: firstly, extracting mRNA (messenger ribonucleic acid) of pan-tissue of a mouse, and then obtaining a cDNA (complementary deoxyribonucleic acid) library by adopting a modified random primer or an oligo-dT primer; carrying out homogenization treatment on the mouse protein library; the method comprises the following steps: transforming plasmids of a BACTH bacteria double-hybrid system to obtain transformed plasmids; carrying out homologous recombination on the transformed plasmids of the sample library and the double hybrid system, and introducing into DHM1 escherichia coli for screening to obtain positive PPI clone with a mutual composition library; and carrying out single-cell transcriptome sequencing on the screened clones based on random primers to construct the mouse protein interaction network. The method is used for carrying out high-throughput screening on mice after thousands of positive PPI combinatorial clones are obtained by'library-to-library 'bacteria or yeast double hybrids, and identifying the same Barcode cDNA combinatorial pairs to realize PPI network identification in different species, among species and in hybridization technology system extensive scenes.
Owner:LIANGZHU LAB

Target screening method of traditional Chinese medicine phellinus linteus and application of phellinus linteus in treatment of HPV positive tumors

The invention discloses a screening method of action targets of traditional Chinese medicine phellinus linteus and application of the screening method to treatment of HPV positive tumors, and the screening method comprises the following steps: (1) screening potential action targets of phellinus linteus, respectively obtaining pathogenic targets of HPV infected cervical cancer by combining a GeneCards database, an OMIM database and a DisGeNET database, and taking intersection to obtain common targets; (2) obtaining a protein-protein interaction network of the intersection targets by using an STRING database, and constructing a PPI network between the intersection targets; (3) carrying out GO function enrichment and KEGG pathway enrichment analysis on the core target spot; and (4) carrying out molecular docking on the identified potential target spot of the phellinus linteus. The traditional Chinese medicine phellinus linteus ketone screened by the method disclosed by the invention can accurately target HPV virus, promote degradation of key oncoprotein E6 / E7 and play an anti-tumor role by regulating mitochondrial autophagy and reducing growth and metastasis of HPV-induced cervical cancer, and the medicine is identified to be low in cost and small in toxic and side effects and has relatively good treatment potential in HPV positive tumors.
Owner:重庆西部数智医疗研究院 +3

Peripheral blood mononuclear cell gene co-expression network-based sepsis marker screening method

The invention relates to the technical field of biomedicine, in particular to a sepsis marker screening method based on a peripheral blood mononuclear cell gene co-expression network, and the method comprises the following steps: obtaining a sample; carrying out batch RNA sequencing, differential expression analysis, weighted gene co-expression network analysis, cross analysis and protein interaction network analysis on the sample, and screening hub genes; performing function enrichment analysis and immune cell infiltration analysis on the hub gene, and screening out a core gene; and carrying out expression verification and clinical correlation analysis on the hub gene. Starting from the overall perspective of a gene network, the screened Hub gene has higher biological significance and reliability, through cross screening of WGCNA and differential expression analysis, the range of candidate genes is greatly narrowed, the screening efficiency and accuracy are improved, bioinformatics analysis, scRNA-seq cell localization and protein level experimental verification are integrated, and the screening method has the advantages that the screening efficiency is greatly improved, and the screening cost is reduced. A complete evidence chain is formed, and the credibility of the marker is ensured.
Owner:THE FIRST MEDICAL CENT CHINESE PLA GENERAL HOSPITAL

Identification method of low-temperature compost energy metabolism core protein

PendingCN122050493ASystem identificationComprehensive recognitionBio-organic fraction processingEnsemble learningBiotechnologyMicroorganism
The invention discloses an identification method of low-temperature compost energy metabolism core protein, and belongs to the technical field of protein screening. In order to solve the problems of single screening dimension, inaccurate key protein identification and unclear mechanism analysis in the prior art, the invention provides a low-temperature compost energy metabolism core protein identification method, which comprises the following steps of: acquiring protein expression data of a low-temperature microorganism sample by utilizing a macro proteomics sequencing technology, screening differential expression proteins based on a set threshold value, and identifying a low-temperature compost energy metabolism core protein. The method comprises the following steps: identifying proteins in a significant enrichment pathway through GO function annotation and KEGG pathway enrichment analysis, carrying out importance ranking on proteins in significant enrichment related pathways by using a random forest model, screening key proteins in combination with the connectivity and network centrality of a protein interaction network, and finally identifying the energy metabolism core proteins in the low-temperature compost. The identification method provided by the invention has the advantages of strong systematicness, high screening accuracy, wide applicability and the like, and can provide key technical support for efficiency improvement and mechanism analysis of low-temperature compost.
Owner:NORTHEAST AGRICULTURAL UNIVERSITY

Fusion network representation and deep learning-based efficacy evaluation method for traditional chinese medicine in colorectal cancer

The application discloses a method for evaluating the curative effect of traditional Chinese medicine in colorectal cancer by fusing network representation and deep learning. The application accurately identifies disease core driver genes through single-cell transcriptome differential analysis and protein-protein interaction network topology centrality index, simultaneously extracts the structural characteristics of traditional Chinese medicine ingredients by graph isomorphism network, constructs traditional Chinese medicine-compound isomorphism network, and extracts the isomorphism topological representation of traditional Chinese medicine by network representation algorithm. The one-dimensional convolutional neural network is used to deeply mine the protein sequence nature semantic features of disease gene sequence, so that the protein features and the end dimension of traditional Chinese medicine are aligned. Finally, the cross-modal joint vector is constructed through feature splicing, and the intervention probability output by the full connection neural network is used to realize the scoring of the candidate drug. The application establishes a direct and quantitative connection between the traditional Chinese medicine intervention space and the single-cell pathological mechanism, realizes the end-to-end evaluation of the anti-colorectal cancer efficacy of traditional Chinese medicine, and can be applied to the fields of traditional Chinese medicine screening and individualized drug administration scheme making.
Owner:HANGZHOU NORMAL UNIVERSITY

Method for analyzing action target of artemisinin for treating renal clear cell carcinoma based on network pharmacology and molecular docking technology

PendingCN121366628ADrug referencesInstrumentsDiseaseProtein protein interaction network
The invention belongs to the technical field of biological medicine, and discloses a method for analyzing an action target of artemisinin for treating renal clear cell carcinoma based on network pharmacology and a molecular docking technology, and the method comprises the following steps: S1, screening the action target of an artemisinin active component; s2, identifying candidate disease targets; s3, acquiring an intersection target point; s4, constructing a protein-protein interaction network and performing network topology analysis; s5, core target biological function and molecular action signal path analysis and visualization; s6, constructing an artemisinin-renal clear cell carcinoma-target spot-pathway network diagram; s7, exploring an action mechanism of artemisinin for improving the renal clear cell carcinoma based on a molecular docking technology; s8, carrying out survival analysis on the core target spot based on the TCGA database, and drawing a Kaplan-Meier curve; and S9, observing the influence of artemisinin and derivatives thereof on the activity of renal clear cell carcinoma 786-O cells by adopting a CCK-8 method. Network pharmacology and molecular docking technologies are applied, multiple omics data are integrated from the perspective of system biology, a drug-target-disease network is constructed, the interaction between artemisinin and renal clear cell carcinoma related targets is deeply analyzed, and the action mechanism of artemisinin on the aspects of genes, proteins, signal channels and the like is comprehensively revealed.
Owner:NANTONG UNIV

Method for identifying cancer driver modules based on graph embedding and hierarchical clustering

This invention discloses a method for identifying cancer-driving modules based on graph embedding and hierarchical clustering, comprising the following steps: 1) setting a model; 2) constructing a weighted network; 3) extracting features of the weighted protein-protein interaction network (PPI) using graph embedding technology; 4) clustering the feature vectors; and 5) constructing a set of driving modules. This method identifies driving modules more effectively and accurately, and identifies driving modules with higher coverage and mutual exclusivity, while also detecting missed cancer-related genes.
Owner:GUANGXI NORMAL UNIV

SNP (Single Nucleotide Polymorphism) molecular marker, primer, kit and method for breeding oriental vole ovarian cancer line

The invention relates to the technical field of molecular biology and animal model genetic breeding, in particular to an SNP (Single Nucleotide Polymorphism) molecular marker, a primer, a kit and a method for breeding an Oriental vole ovarian cancer line. Firstly, a method for accurately screening the risk SNP marker by integrating transcriptome sequencing, Wei-Fst population genetic analysis and protein interaction network core node screening is provided, and a specific detection primer group and a kit thereof are provided. Secondly, the invention also provides a method for performing risk prediction through a weighted random forest model by using the marker and the kit so as to realize efficient directional breeding, and the occurrence rate of the spontaneous ovarian cancer of the oriental vole can be obviously improved from about 4% to 44.3%, so that the high-incidence strain of the spontaneous ovarian cancer of the oriental vole can be rapidly and directionally cultured, and the breeding efficiency is improved. And a key animal model resource is provided for research of ovarian cancer.
Owner:CENT SOUTH UNIV

Serum biomarkers for diagnosis and disease activity assessment of takayasu arteritis and application thereof

The application provides serum biomarkers for diagnosing and evaluating the activity of aortitis and application, and relates to the field of disease activity evaluation. The serum biomarkers are serum proteins: HP and ORM1. HP and ORM1 are determined as two new serum biomarkers through comprehensive proteomics analysis; gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis are carried out using a DAVID database; a protein-protein interaction network is constructed using Metascape. A random forest model is trained using a caret package, and a nomogram is visualized using an rms package. Serum samples are obtained, and the serum levels of HP and ORM1 are determined using a commercial ELISA kit; they are significantly related to disease activity, and are involved in inflammation / immune processes in aortitis, so the markers have the potential to serve as an auxiliary tool for monitoring the activity of aortitis.
Owner:THE FIRST AFFILIATED HOSPITAL OF MEDICAL COLLEGE OF XIAN JIAOTONG UNIV