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Similarity measurement method and device of gene module group, electronic equipment and storage medium

A similarity measurement and storage medium technology, which is applied in the field of similarity measurement methods of electronic equipment and storage media, devices, and gene module groups, can solve the problem that the similarity results cannot accurately measure the similarity of gene module groups, and achieve accurate similarity effect

Active Publication Date: 2022-01-18
DALI UNIV
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Problems solved by technology

However, since gene interaction is a common genetic phenomenon in organisms, any biological hereditary trait is usually the result of the interaction of many different genes, and the similarity results obtained by only considering the genes themselves cannot accurately measure the relationship between gene module groups similarity of

Method used

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  • Similarity measurement method and device of gene module group, electronic equipment and storage medium
  • Similarity measurement method and device of gene module group, electronic equipment and storage medium
  • Similarity measurement method and device of gene module group, electronic equipment and storage medium

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Embodiment 1

[0067] First, the miRNA and mRNA expression profile data of breast cancer matched samples were obtained from the cancer gene expression profile database TCGA (The Cancer GenomeAtla). After removing duplicates and miRNAs and mRNAs without gene names, 894 miRNAs from 690 breast cancer matching samples were obtained, denoted as D 1 ={G 1,1 ;G 1,2 ;…;G 1,690}∈R 690×894 , also obtained 19068 mRNA expression profile data, denoted as D 2 ={G 2,1 ;G 2,2 ;…;G 2,690}∈R 690×19068 , in this example, gene represents miRNA or mRNA.

[0068] Then, breast cancer subtypes can be predicted based on the acquired gene expression profile data.

[0069] Based on the above breast cancer data, 690 breast cancer samples were divided into five subtypes using the PAM50 molecular subtype classification model: LuminalA type (LumA), LuminalB type (LumB), basal cell type (Basal), HER2 overexpression type ( Her2) and normal gene expression type (Normal). The number of breast cancer samples of LumA...

Embodiment 2

[0086] In this embodiment, the process of obtaining gene expression profile data is the same as that in Embodiment 1, and details are not repeated here.

[0087] In this embodiment, five clustering methods (including WGCNA method, K-means clustering method, hierarchical clustering method, FCM clustering method and FABIA double-clustering factor analysis method) were used based on the obtained gene expression profile data, respectively. Identify co-expression modules of genes. Among them, the minimum scale-free topology fitting index R in the WGCNA method 2 It is set to 0.8, the maximum number of clusters of K-means clustering method, hierarchical clustering method, FCM clustering method and FABIA bi-clustering factor analysis method is set to 10, and other parameters are default settings. The number of miRNAs or mRNAs in each miRNA or mRNA co-expression module is not less than 3. Five methods identified five miRNA co-expression module groups in breast cancer miRNA expression...

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Abstract

The invention provides a similarity measurement method and a device of a gene module group, electronic equipment and a storage medium, and relates to the technical field of gene recognition. The similarity measurement method for the gene module groups comprises the following steps: collecting a first gene module group and a second gene module group; calculating the similarity between the first gene module and the second gene module according to a formula; and calculating the similarity of the first gene module group and the second gene module group according to the gene module similarity of the first gene module and the second gene module. According to the method, based on a given formula, when the similarity between the first gene module group and the second gene module group is calculated, the gene interaction relation is considered, and the similarity between different gene module groups can be measured more accurately.

Description

technical field [0001] The invention relates to the technical field of gene identification, in particular to a method, device, electronic equipment and storage medium for measuring the similarity of gene module groups. Background technique [0002] A gene is a deoxyribonucleic acid (Deoxyribonucleic Acid, DNA) or ribonucleic acid (Ribonucleic Acid, RNA) fragment containing genetic information, which controls all hereditary traits of an organism. Through the process of replication, transcription and translation, genes complete important biological processes such as cell differentiation, cell proliferation, cell growth and protein synthesis. Gene modules are of great significance for exploring human physiological and pathological processes. Gene modules exhibit specificity in different biological conditions, different biological tissues, different tumor subtypes, and different cells. [0003] By calculating the similarity of gene module groups, it is possible to understand t...

Claims

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Application Information

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IPC IPC(8): G06K9/62G16B25/10
CPCG16B25/10G06F18/23G06F18/22
Inventor 张俊鹏赵春文李司婧杨燕婷
Owner DALI UNIV
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