Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma.

Content Provider	Europe PMC
Author	Li, Jianguo Zhou, Jin Kai, Shuangshuang Wang, Can Wang, Daijun Jiang, Jiying
Copyright Year	2020
Abstract	Hepatocellular carcinoma (HCC) is a primary liver cancer associated with a growing incidence and extremely high mortality. However, the pathogenic mechanism is still not fully understood. In the present study, we identified 1,631 upregulated and 1,515 downregulated genes and found that cell cycle and metabolism-related pathways or biological processes highly dysregulated in HCC. To assess the biological importance of these DEGs, we carried out weighted gene coexpression network analysis (WGCNA) to identify the functional modules potentially involved in HCC pathogenesis or progression. The five modules were detected with Dynamic Tree Cut algorithm, and GO enrichment analysis revealed that these modules exhibited different biological processes or signaling pathways, such as metabolism-related pathways, cell proliferation-related pathways, and molecules in tumor microenvironment. Moreover, we also observed two immune cells, namely, cytotoxic cells and macrophage enriched in modules grey and brown, respectively, while T helper cell-2 (Th2) was enriched in module turquoise. Among the WGCNA network, four hub long noncoding RNAs (lncRNAs) were identified to be associated with HCC prognostic outcomes, suggesting that coexpression network analysis could uncover lncRNAs with functional importance, which may be associated with prognostic outcomes of HCC patients. In summary, this study demonstrated that network-based analysis could identify some functional modules and some hub-lncRNAs, which may be critical for HCC pathogenesis or progression.
ISSN	23146133
Journal	Biomed Research International
Volume Number	2020
PubMed Central reference number	PMC7559504
PubMed reference number	33083449
e-ISSN	23146141
DOI	10.1155/2020/1371632
Language	English
Publisher	Hindawi
Publisher Date	2020-10-06
Access Restriction	Open
Rights License	This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copyright © 2020 Jianguo Li et al.
Content Type	Text
Resource Type	Article
Subject	Immunology and Microbiology Medicine Biochemistry, Genetics and Molecular Biology