A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host
Abstract Background Influenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researcher...
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| Format: | Article |
| Language: | English |
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BMC
2020-07-01
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| Series: | BMC Infectious Diseases |
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| Online Access: | http://link.springer.com/article/10.1186/s12879-020-05214-0 |
| _version_ | 1818240765663379456 |
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| author | Qurat ul Ain Farooq Zeeshan Shaukat Sara Aiman Tong Zhou Chunhua Li |
| author_facet | Qurat ul Ain Farooq Zeeshan Shaukat Sara Aiman Tong Zhou Chunhua Li |
| author_sort | Qurat ul Ain Farooq |
| collection | DOAJ |
| description | Abstract Background Influenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researchers can explore the virus invasion into the host cells by studying the virus-host relationship based on their protein-protein interaction network. Methods In this study, we present a comprehensive IAV-host protein-protein interaction network that is obtained based on the literature-curated protein interaction datasets and some important interaction databases. The network is constructed in Cytoscape and analyzed with its plugins including CytoHubba, CytoCluster, MCODE, ClusterViz and ClusterOne. In addition, Gene Ontology and KEGG enrichment analyses are performed on the highly IAV-associated human proteins. We also compare the current results with those from our previous study on Hepatitis C Virus (HCV)-host protein-protein interaction network in order to find out valuable information. Results We found out 1027 interactions among 829 proteins of which 14 are viral proteins and 815 belong to human proteins. The viral protein NS1 has the highest number of associations with human proteins followed by NP, PB2 and so on. Among human proteins, LNX2, MEOX2, TFCP2, PRKRA and DVL2 have the most interactions with viral proteins. Based on KEGG pathway enrichment analysis of the highly IAV-associated human proteins, we found out that they are enriched in the KEGG pathway of basal cell carcinoma. Similarly, the result of KEGG analysis of the common host factors involved in IAV and HCV infections shows that these factors are enriched in the infection pathways of Hepatitis B Virus (HBV), Viral Carcinoma, measles and certain other viruses. Conclusion It is concluded that the list of proteins we identified might be used as potential drug targets for the drug design against the infectious diseases caused by Influenza A Virus and other viruses. |
| first_indexed | 2024-12-12T13:18:39Z |
| format | Article |
| id | doaj.art-d29d2a9c512e4ea0aa4bc096e87a002c |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-12-12T13:18:39Z |
| publishDate | 2020-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-d29d2a9c512e4ea0aa4bc096e87a002c2022-12-22T00:23:22ZengBMCBMC Infectious Diseases1471-23342020-07-0120111010.1186/s12879-020-05214-0A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its hostQurat ul Ain Farooq0Zeeshan Shaukat1Sara Aiman2Tong Zhou3Chunhua Li4Faculty of Environmental and Life Sciences, Beijing University of TechnologyFaculty of Information Technology, Beijing University of TechnologyFaculty of Environmental and Life Sciences, Beijing University of TechnologyFaculty of Environmental and Life Sciences, Beijing University of TechnologyFaculty of Environmental and Life Sciences, Beijing University of TechnologyAbstract Background Influenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researchers can explore the virus invasion into the host cells by studying the virus-host relationship based on their protein-protein interaction network. Methods In this study, we present a comprehensive IAV-host protein-protein interaction network that is obtained based on the literature-curated protein interaction datasets and some important interaction databases. The network is constructed in Cytoscape and analyzed with its plugins including CytoHubba, CytoCluster, MCODE, ClusterViz and ClusterOne. In addition, Gene Ontology and KEGG enrichment analyses are performed on the highly IAV-associated human proteins. We also compare the current results with those from our previous study on Hepatitis C Virus (HCV)-host protein-protein interaction network in order to find out valuable information. Results We found out 1027 interactions among 829 proteins of which 14 are viral proteins and 815 belong to human proteins. The viral protein NS1 has the highest number of associations with human proteins followed by NP, PB2 and so on. Among human proteins, LNX2, MEOX2, TFCP2, PRKRA and DVL2 have the most interactions with viral proteins. Based on KEGG pathway enrichment analysis of the highly IAV-associated human proteins, we found out that they are enriched in the KEGG pathway of basal cell carcinoma. Similarly, the result of KEGG analysis of the common host factors involved in IAV and HCV infections shows that these factors are enriched in the infection pathways of Hepatitis B Virus (HBV), Viral Carcinoma, measles and certain other viruses. Conclusion It is concluded that the list of proteins we identified might be used as potential drug targets for the drug design against the infectious diseases caused by Influenza A Virus and other viruses.http://link.springer.com/article/10.1186/s12879-020-05214-0Influenza a virusHepatitis C virusProtein-protein interaction networksCytoscapeKEGG |
| spellingShingle | Qurat ul Ain Farooq Zeeshan Shaukat Sara Aiman Tong Zhou Chunhua Li A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host BMC Infectious Diseases Influenza a virus Hepatitis C virus Protein-protein interaction networks Cytoscape KEGG |
| title | A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host |
| title_full | A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host |
| title_fullStr | A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host |
| title_full_unstemmed | A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host |
| title_short | A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host |
| title_sort | systems biology driven approach to construct a comprehensive protein interaction network of influenza a virus with its host |
| topic | Influenza a virus Hepatitis C virus Protein-protein interaction networks Cytoscape KEGG |
| url | http://link.springer.com/article/10.1186/s12879-020-05214-0 |
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