System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach
Background. KDM6A (Lysine (K)-Specific Demethylase 6A) is the driver gene related to esophageal squamous cell carcinoma (ESCC). In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and...
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| Format: | Article |
| Language: | English |
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Wiley
2016-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1155/2016/1970904 |
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| author | Jihua Ran Hui Li Huiwu Li |
| author_facet | Jihua Ran Hui Li Huiwu Li |
| author_sort | Jihua Ran |
| collection | DOAJ |
| description | Background. KDM6A (Lysine (K)-Specific Demethylase 6A) is the driver gene related to esophageal squamous cell carcinoma (ESCC). In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and follow it to review its biological function. Method. We constructed a PPI network with Cytoscape software and performed clustering of network with Clust&See. Then, we evaluate the pathways, which are statistically involved in the network derived from KDM6A. Lastly, gene ontology analysis of clusters of genes in the network was conducted. Result. The network includes three clusters that consist of 74 nodes connected via 453 edges. Fifty-five pathways are statistically involved in the network and most of them are functionally related to the processes of cell cycle, gene expression, and carcinogenesis. The biology themes of clusters 1, 2, and 3 are chromatin modification, regulation of gene expression by transcription factor complex, and control of cell cycle, respectively. Conclusion. The PPI network presents a panoramic view which can facilitate for us to understand the function role of KDM6A. It is a helpful way by network approach to perform system review on a certain gene. |
| format | Article |
| id | doaj-art-dea9bcfb702a4db0b8ff60781dc73ea3 |
| institution | Kabale University |
| issn | 2356-6140 1537-744X |
| language | English |
| publishDate | 2016-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-dea9bcfb702a4db0b8ff60781dc73ea32025-02-03T05:54:21ZengWileyThe Scientific World Journal2356-61401537-744X2016-01-01201610.1155/2016/19709041970904System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology ApproachJihua Ran0Hui Li1Huiwu Li2Department of Biochemistry and Molecular Biology, School of Basic Medicine, Xinjiang Medical University, 393 Xinyi Road, Urumqi, Xinjiang 830054, ChinaCentral Laboratory of Xinjiang Medical University, 393 Xinyi Road, Urumqi, Xinjiang 830054, ChinaDepartment of Biochemistry and Molecular Biology, School of Basic Medicine, Xinjiang Medical University, 393 Xinyi Road, Urumqi, Xinjiang 830054, ChinaBackground. KDM6A (Lysine (K)-Specific Demethylase 6A) is the driver gene related to esophageal squamous cell carcinoma (ESCC). In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and follow it to review its biological function. Method. We constructed a PPI network with Cytoscape software and performed clustering of network with Clust&See. Then, we evaluate the pathways, which are statistically involved in the network derived from KDM6A. Lastly, gene ontology analysis of clusters of genes in the network was conducted. Result. The network includes three clusters that consist of 74 nodes connected via 453 edges. Fifty-five pathways are statistically involved in the network and most of them are functionally related to the processes of cell cycle, gene expression, and carcinogenesis. The biology themes of clusters 1, 2, and 3 are chromatin modification, regulation of gene expression by transcription factor complex, and control of cell cycle, respectively. Conclusion. The PPI network presents a panoramic view which can facilitate for us to understand the function role of KDM6A. It is a helpful way by network approach to perform system review on a certain gene.http://dx.doi.org/10.1155/2016/1970904 |
| spellingShingle | Jihua Ran Hui Li Huiwu Li System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach The Scientific World Journal |
| title | System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach |
| title_full | System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach |
| title_fullStr | System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach |
| title_full_unstemmed | System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach |
| title_short | System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach |
| title_sort | system review about function role of escc driver gene kdm6a by network biology approach |
| url | http://dx.doi.org/10.1155/2016/1970904 |
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