Network analyses elucidate the role of SMYD3 in esophageal squamous cell carcinoma
| Autor: | En-Min Li, Yue Li, Ying Zhu, Li-Yan Xu, Jian-Yi Wu, Bing-Li Wu, Xinning Liu, Simin Guo, Chuhong Chen, Zhennan Liao, Hai-Ying Zou, Wenming Xie, Zhoude Zheng, Pi-Xian Zhang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
YAP1 Genetics Gene knockdown SMYD3 Protein family GATA3 Computational biology Cell cycle Biology medicine.disease_cause General Biochemistry Genetics and Molecular Biology 03 medical and health sciences 030104 developmental biology 0302 clinical medicine 030220 oncology & carcinogenesis Gene expression medicine protein–protein interaction network Carcinogenesis Gene Research Articles Research Article functional enrichment annotation |
| Zdroj: | FEBS Open Bio |
| ISSN: | 2211-5463 |
| Popis: | SMYD3 is a member of the SET and myeloid-Nervy-DEAF-1 (MYND) domain-containing protein family of methyltransferases, which are known to play critical roles in carcinogenesis. Expression of SMYD3 is elevated in various cancers, including esophageal squamous cell carcinoma (ESCC), and is correlated with the survival time of patients with ESCC. Here, we dissect gene expression data, from a previously described KYSE150 ESCC cell line in which SMYD3 had been knocked down, by integration with the protein-protein interaction (PPI) network, to find the new potential biological roles of SMYD3 and subsequent target genes. By construction of a specific PPI network, differentially expressed genes (DEGs), following SMYD3 knockdown, were identified as interacting with thousands of neighboring proteins. Enrichment analyses from the DAVID Functional Annotation Chart found significant Gene Ontology (GO) terms associated with transcription activities, which were closely related to SMYD3 function. For example, YAP1 and GATA3 might be a target gene for SMYD3 to regulate transcription. Enrichment annotation of the total DEG PPI network by GO 'Biological Process' generated a connected functional map and found 532 significant terms, including known and potential biological roles of SMYD3 protein, such as expression regulation, signal transduction, cell cycle, cell metastasis, and invasion. Subcellular localization analyses found that DEGs and their interacting proteins were distributed in multiple layers, which might reflect the intricate biological processes at the spatial level. Our analysis of the PPI network has provided important clues for future detection of the biological roles and mechanisms, as well as the target genes of SMYD3. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Plný text