tetano
Editor, Senior Moderator
Eur J Med Res
. 2021 Dec 17;26(1):146.
doi: 10.1186/s40001-021-00609-4.
An integrative bioinformatics analysis for identifying hub genes associated with infection of lung samples in patients infected with SARS-CoV-2
Tian-Ao Xie[SUP] #[/SUP][SUP] 1 2 [/SUP], Zhi-Jian He[SUP] #[/SUP][SUP] 1 2 [/SUP], Chuan Liang[SUP] #[/SUP][SUP] 1 2 [/SUP], Hao-Neng Dong[SUP] 1 2 [/SUP], Jie Zhou[SUP] 1 2 [/SUP], Shu-Jin Fan[SUP] 1 2 [/SUP], Xu-Guang Guo[SUP] 3 4 5 6 [/SUP]
Affiliations
Abstract
Background: At the end of 2019, the world witnessed the emergence and ravages of a viral infection induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Also known as the coronavirus disease 2019 (COVID-19), it has been identified as a public health emergency of international concern (PHEIC) by the World Health Organization (WHO) because of its severity.
Methods: The gene data of 51 samples were extracted from the GSE150316 and GSE147507 data set and then processed by means of the programming language R, through which the differentially expressed genes (DEGs) that meet the standards were screened. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on the selected DEGs to understand the functions and approaches of DEGs. The online tool STRING was employed to construct a protein-protein interaction (PPI) network of DEGs and, in turn, to identify hub genes.
Results: A total of 52 intersection genes were obtained through DEG identification. Through the GO analysis, we realized that the biological processes (BPs) that have the deepest impact on the human body after SARS-CoV-2 infection are various immune responses. By using STRING to construct a PPI network, 10 hub genes were identified, including IFIH1, DDX58, ISG15, EGR1, OASL, SAMD9, SAMD9L, XAF1, IFITM1, and TNFSF10.
Conclusion: The results of this study will hopefully provide guidance for future studies on the pathophysiological mechanism of SARS-CoV-2 infection.
Keywords: Differentially expressed genes; Hub genes; Protein–protein interactions network; SARS-CoV-2.
. 2021 Dec 17;26(1):146.
doi: 10.1186/s40001-021-00609-4.
An integrative bioinformatics analysis for identifying hub genes associated with infection of lung samples in patients infected with SARS-CoV-2
Tian-Ao Xie[SUP] #[/SUP][SUP] 1 2 [/SUP], Zhi-Jian He[SUP] #[/SUP][SUP] 1 2 [/SUP], Chuan Liang[SUP] #[/SUP][SUP] 1 2 [/SUP], Hao-Neng Dong[SUP] 1 2 [/SUP], Jie Zhou[SUP] 1 2 [/SUP], Shu-Jin Fan[SUP] 1 2 [/SUP], Xu-Guang Guo[SUP] 3 4 5 6 [/SUP]
Affiliations
- PMID: 34920753
- DOI: 10.1186/s40001-021-00609-4
Abstract
Background: At the end of 2019, the world witnessed the emergence and ravages of a viral infection induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Also known as the coronavirus disease 2019 (COVID-19), it has been identified as a public health emergency of international concern (PHEIC) by the World Health Organization (WHO) because of its severity.
Methods: The gene data of 51 samples were extracted from the GSE150316 and GSE147507 data set and then processed by means of the programming language R, through which the differentially expressed genes (DEGs) that meet the standards were screened. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on the selected DEGs to understand the functions and approaches of DEGs. The online tool STRING was employed to construct a protein-protein interaction (PPI) network of DEGs and, in turn, to identify hub genes.
Results: A total of 52 intersection genes were obtained through DEG identification. Through the GO analysis, we realized that the biological processes (BPs) that have the deepest impact on the human body after SARS-CoV-2 infection are various immune responses. By using STRING to construct a PPI network, 10 hub genes were identified, including IFIH1, DDX58, ISG15, EGR1, OASL, SAMD9, SAMD9L, XAF1, IFITM1, and TNFSF10.
Conclusion: The results of this study will hopefully provide guidance for future studies on the pathophysiological mechanism of SARS-CoV-2 infection.
Keywords: Differentially expressed genes; Hub genes; Protein–protein interactions network; SARS-CoV-2.