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Application of transcriptomics for co-expressing cyclic circadian rhythm to discovery of drug action mechanism

A technology of drug action and circadian rhythm, which can be used in chemical property prediction, chemical process analysis/design, molecular entity identification, etc.

Inactive Publication Date: 2019-01-11
NANKAI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The differential expression changes of genes will change over time, that is, the differential expression analysis of transcriptome at a single time point cannot effectively explore the mechanism of action of drugs

Method used

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  • Application of transcriptomics for co-expressing cyclic circadian rhythm to discovery of drug action mechanism
  • Application of transcriptomics for co-expressing cyclic circadian rhythm to discovery of drug action mechanism
  • Application of transcriptomics for co-expressing cyclic circadian rhythm to discovery of drug action mechanism

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0041] Example 1: Discovery process route for drug action mechanism of co-expression cycle circadian rhythm transcriptomics

[0042] The research platform for the mechanism of action between drugs and organisms with drug-biological phenotypes is: use mRNA expression data to construct mRNA expression networks and divide them into modules, and then use hypergeometric distribution to enrich the functions of GO functions and KEGG pathways for each module Analysis, and then extract the module that overcomes its own cycle rhythm as the main explanation of the internal molecular mechanism of the corresponding drug treatment-related biological phenotype changes, and finally integrate the phenotypic changes and functional analysis after drug treatment and use data visualization to carry out the physiological effects of drugs on the corresponding biological phenotypes The molecular mechanism of the function is fully explained and evaluated; this process route can also be used to study th...

Embodiment 2

[0043] Example 2: A method for discovering the mechanism of action of a pesticide, taking the mechanism of coronatin as an example of inhibiting growth and promoting defense

[0044] In this example, the present invention is applied to the mRNA expression data of the two-week-old Arabidopsis seedlings treated with coronatin to cause the growth of the seedlings to stop, and the resistance to pathogenic bacteria and insect pests to be enhanced. The time span is 0h, 0.25h, 0.5h, 1h, 1.5h, 2h, 2.5h, 3h, 4h, 5h, 6h, 7h, 8h, 10h, 12h, 14h, 16h, 18h, 20h, 22h, 24h, h is the abbreviation of time hours. According to the drug treatment, the samples were divided into the control group, the control group was represented by mock and the experimental group, and the experimental group was represented by COR, and the common gene co-expression network of the control group and the treatment group was constructed by using the WGCNA method.

[0045] See the attached manual for the specific proces...

Embodiment 3

[0058] Example 3: Transcriptomics of Co-expression Periodic Circadian Rhythm to Explore the Mechanism of Drug Action and Its Process Route and Operation Steps Used in the Field of Medicine to Discover the Mechanism of Drug Action

[0059] Using the experimental medical animal and human mRNA expression data to construct the mRNA expression network and divide it into modules, then use the hypergeometric distribution to analyze the GO function and KEGG pathway function enrichment of each module, and then extract the module that overcomes its own cycle rhythm as the corresponding medical treatment The main explanation of the internal molecular mechanism of the phenotypic changes of related experimental medicine animals and humans. Finally, the phenotypic changes and functional analysis after comprehensive medical treatment and the use of data visualization are used to fully explain the molecular mechanisms of the corresponding experimental medicine animals and human physiological fu...

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Abstract

The invention provides a method for discovering a drug action mechanism by transcriptomics for co-expressing cyclic circadian rhythm. The method comprises the steps: successfully identifying a molecular mechanism of a drug action by analyzing deep sequencing circadian time sequence transcriptome data in combination with bioinformatics, coexpression analysis, machine learning and data visualizationtechnologies; and establishing an mRNA expression network by utilizing mRNA expression data, dividing modules, carrying out functional enrichment analysis on GO and KEGG of each module by utilizing hypergeometric distribution, extracting the module overcoming the cyclic rhythm of the module as a main explanation for an endogenous molecular mechanism of biological phenotype change related to corresponding drug treatment, and comprehensively explaining and assessing the molecular mechanism of a drug for a physiological function of a corresponding biological representation by utilizing data visualization in combination with phenotypic change and functional analysis after drug treatment. The invention further provides an application of the method to the research of an action mechanism of coronatine inhibiting growth and promoting defense and the discovery of action mechanisms and toxic / side effect mechanisms of pesticides, medicines, veterinary drugs and drugs for aquatic products.

Description

technical field [0001] The invention relates to the technical field of drug action mechanism research and omics big data analysis, in particular, relates to a method for finding drug action mechanism through transcriptomic gene clustering and classification of co-expression cycle circadian rhythm. Background technique [0002] The methods currently used to study the mechanism of action (MoA) of drugs mainly fall into two categories. The first approach includes several strategies that rely on model organisms associated with genetic manipulation, but many drugs may not exhibit activity in these model organisms, likely due to multiple resistance mechanisms and target differences. The second type of method is based on the binding affinity of the drug to the protein, such as affinity purification or affinity chromatography. These methods require prior knowledge of the structure-activity relationship of the drug and reasonable abundance of the target protein in the organism rathe...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16C20/10G16C20/20G16C20/30
Inventor 范志金张乃楼赵斌郭晓凤吴启凡于斌周爽杨冬艳王海英
Owner NANKAI UNIV
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