Dataset Information

Identification of key genes in atrial fibrillation using bioinformatics analysis.

ABSTRACT:

Background

Atrial fibrillation (AF) is one of the most common arrhythmia, which brings huge burden to the individual and the society. However, the mechanism of AF is not clear. This paper aims at screening the key differentially expressed genes (DEGs) of atrial fibrillation and to construct enrichment analysis and protein-protein interaction (PPI) network analysis for these DEGs.

Methods

The datasets were collected from the Gene Expression Omnibus database to extract data of left atrial appendage (LAA) RNA of patients with or without AF in GSE79768, GSE31821, GSE115574, GSE14975 and GSE41177. Batch normalization, screening of the differential genes and gene ontology analysis were finished by R software. Reactome analysis was used for pathway analysis. STRING platform was utilized for PPI network analysis. At last, we performed reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to validate the expression of key genes in 20 sinus rhythm (SR) LAA tissues and 20 AF LAA tissues.

Results

A total of 106 DEGs were screened in the merged dataset. Among these DEGs, 74 genes were up-regulated and 32 genes down-regulated. DEGs were mostly enriched in extracellular matrix organization, protein activation cascade and extracellular structure organization. In PPI network, we identified SPP1, COL5A1 and VCAN as key genes which were associated with extracellular matrix. RT-qPCR showed the same expression trend of the three key genes as in our bioinformatics analysis. The expression levels of SPP1, COL5A1 and VCAN were increased in AF tissues compared to SR tissues (P < 0.05).

Conclusion

According to the analyses which were conducted by bioinformatics tools, genes related to extracellular matrix were involved in pathology of AF and may become the possible targets for the diagnosis and treatment of AF.

SUBMITTER: Liu Y

PROVIDER: S-EPMC7419195 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Publications

Identification of key genes in atrial fibrillation using bioinformatics analysis.

Liu Yueheng Y Tang Rui R Zhao Ye Y Jiang Xuan X Wang Yuchao Y Gu Tianxiang T

BMC cardiovascular disorders 20200810 1

<h4>Background</h4>Atrial fibrillation (AF) is one of the most common arrhythmia, which brings huge burden to the individual and the society. However, the mechanism of AF is not clear. This paper aims at screening the key differentially expressed genes (DEGs) of atrial fibrillation and to construct enrichment analysis and protein-protein interaction (PPI) network analysis for these DEGs.<h4>Methods</h4>The datasets were collected from the Gene Expression Omnibus database to extract data of left ...[more]

PMID: 32778054

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Dataset Information

Identification of key genes in atrial fibrillation using bioinformatics analysis.

Background

Methods

Results

Conclusion

Publications

Identification of key genes in atrial fibrillation using bioinformatics analysis.

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