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Gene expression data analysis method based on PAM clustering algorithm

A technology for gene expression and data analysis, applied in the field of data analysis

Pending Publication Date: 2021-09-10
吉林省蒲川生物医药有限公司
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Problems solved by technology

[0008] In order to solve the technical problems existing in the existing gene module identification method, the present invention provides a gene expression data analysis method based on the PAM clustering algorithm

Method used

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  • Gene expression data analysis method based on PAM clustering algorithm
  • Gene expression data analysis method based on PAM clustering algorithm
  • Gene expression data analysis method based on PAM clustering algorithm

Examples

Experimental program
Comparison scheme
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specific Embodiment approach 1

[0081] Research on the mechanism of action of NSC319726 based on this method

[0082] (1) Preliminary identification results of genes

[0083] In this study, the T test was used to test the expression of each gene in the original data in the treatment group and the control group. After the conditional screening of P<=0.05, a total of 5044 genes with statistical significance were identified for further analysis.

[0084] (2) Use the PAM algorithm to mine functional gene modules

[0085] In this study, the elbow rule was used to further determine the number of clusters ( figure 2 ). Depend on figure 2 It can be seen that the optimal number of clusters in this study is 3. The expression of 5044 genes in the drug-administered group was clustered using the PAM algorithm, and the clustering results are shown in image 3 . Obviously, the 3 clusters obtained by the PAM algorithm are 3 gene modules, the module m1 contains 1599 genes, the module m2 contains 1964 genes, and the ...

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Abstract

The invention discloses a gene expression data analysis method based on a PAM clustering algorithm, and relates to the field of data analysis. The method comprises the steps of data acquisition, data preprocessing, gene module identification, GO enrichment analysis, PPI network construction, HUB gene identification and HUB gene verification. According to the method, on the basis of fully utilizing information contained in gene expression data, the optimal membership module can be searched for each gene through multiple iterations, so that the identified gene module is more reliable. The hidden information contained in the gene module can be better mined, so that the bioinformatics problem to be solved is comprehensively analyzed. According to the method, data preprocessing is performed on the gene expression data, so that the problems of much noise, many irrelevant genes, sparse data and the like in the gene expression data are solved. Through the downstream bioinformatics analysis process, a series of bioinformatics analysis can be completed, and the bioinformatics problems to be solved can be comprehensively analyzed and explained.

Description

technical field [0001] The invention relates to the technical field of data analysis, in particular to a gene expression data analysis method based on a PAM clustering algorithm. Background technique [0002] A gene is a basic unit with genetic information on the chromosome of a biological cell, and the expression of multiple genes in an organism can be measured through a gene chip. The gene chip uses the base pairing principle of DNA, using artificially synthesized base sequences as gene probes to identify specific genes in cells, and mixing cell samples treated with fluorescent labels on the gene chip to make the DNA in the sample The nucleotide fragments are hybridized with the corresponding gene probes. The fluorescence intensity value of each point on the gene chip is obtained by fluorescence imaging, and the fluorescence intensity value reflects the expression level of the corresponding gene in the sample. [0003] Thousands or even tens of thousands of genes are sto...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B25/10G16B40/00G06K9/62
CPCG16B25/10G16B40/00G06F18/23
Inventor 付聪梁磊张彦易星丞许彤
Owner 吉林省蒲川生物医药有限公司
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