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 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.
Department of Biochemistry and Molecular Biology, School of Basic Medicine, Xinjiang Medical University, 393 Xinyi Road, Urumqi, Xinjiang 830054, China; Clinical Laboratory Diagnosis Center of PLA, Urumqi General Hospital, 359 Youhao Road, Urumqi, Xinjiang 830054, China.
Jihua
J
Ran
Central Laboratory of Xinjiang Medical University, 393 Xinyi Road, Urumqi, Xinjiang 830054, China.
Hui
H
Li
Department of Biochemistry and Molecular Biology, School of Basic Medicine, Xinjiang Medical University, 393 Xinyi Road, Urumqi, Xinjiang 830054, China; Cancer Institute, The Affiliated Cancer Hospital of Xinjiang Medical University, 789 East Suzhou Road, Urumqi, Xinjiang Uyghur Autonomous Region 830011, China.
Huiwu
H
Li
D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D016000:Cluster Analysis; D004938:Esophageal Neoplasms / Q000235:genetics*; D000077277:Esophageal Squamous Cell Carcinoma; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D056466:Histone Demethylases / Q000235:genetics*; D006801:Humans; D009687:Nuclear Proteins / Q000235:genetics*; D060066:Protein Interaction Maps; D012984:Software; D049490:Systems Biology
D009687:Nuclear Proteins; D056466:Histone Demethylases; C523998:KDM6A protein, human