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Co-expression analysis of differentially expressed genes in hepatitis C virus-induced hepatocellular carcinoma.

Song Q, Zhao C, Ou S, Meng Z, Kang P, Fan L, Qi F, Ma Y - Mol Med Rep (2014)

Bottom Line: There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h.Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection.In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

View Article: PubMed Central - PubMed

Affiliation: Department of Interventional Radiology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.

ABSTRACT
The aim of the current study was to investigate the molecular mechanisms underlying hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) using the expression profiles of HCV-infected Huh7 cells at different time points. The differentially expressed genes (DEGs) were identified with the Samr package in R software once the data were normalized. Functional and pathway enrichment analysis of the identified DEGs was also performed. Subsequently, MCODE in Cytoscape software was applied to conduct module analysis of the constructed co-expression networks. A total of 1,100 DEGs were identified between the HCV-infected and control samples at 12, 18, 24 and 48 h post-infection. DEGs at 24 and 48 h were involved in the same signaling pathways and biological processes, including sterol biosynthetic processes and tRNA amino-acylation. There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h. Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection. In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

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Specific functional modules of differentially expressed genes at 12, 18 and 24 h post-infection.
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f4-mmr-11-01-0021: Specific functional modules of differentially expressed genes at 12, 18 and 24 h post-infection.

Mentions: All DEGs were the nodes of the co-expression networks. DEGs at 24 and 48 h presented high clustering and were more modular (Table IV). The top 5 modules with a node number >10 were screened out for GO functional analysis by DAVID. The functions of the significantly enriched modules included various biological processes (Figs. 4 and 5). The biological processes of cell proliferation and the cell cycle were decentralized, which suggested that HCV infection may influence the proliferation of host liver cells. The co-expression networks at 18, 24 and 48 h demonstrated that the metabolism and transport processes of multiple biological macromolecules, including amino acids, enzymes and carbohydrates, began to decrease. At 24 and 48 h, tRNA synthesis-related biological processes were emerging, suggesting that replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection.


Co-expression analysis of differentially expressed genes in hepatitis C virus-induced hepatocellular carcinoma.

Song Q, Zhao C, Ou S, Meng Z, Kang P, Fan L, Qi F, Ma Y - Mol Med Rep (2014)

Specific functional modules of differentially expressed genes at 12, 18 and 24 h post-infection.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4237098&req=5

f4-mmr-11-01-0021: Specific functional modules of differentially expressed genes at 12, 18 and 24 h post-infection.
Mentions: All DEGs were the nodes of the co-expression networks. DEGs at 24 and 48 h presented high clustering and were more modular (Table IV). The top 5 modules with a node number >10 were screened out for GO functional analysis by DAVID. The functions of the significantly enriched modules included various biological processes (Figs. 4 and 5). The biological processes of cell proliferation and the cell cycle were decentralized, which suggested that HCV infection may influence the proliferation of host liver cells. The co-expression networks at 18, 24 and 48 h demonstrated that the metabolism and transport processes of multiple biological macromolecules, including amino acids, enzymes and carbohydrates, began to decrease. At 24 and 48 h, tRNA synthesis-related biological processes were emerging, suggesting that replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection.

Bottom Line: There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h.Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection.In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

View Article: PubMed Central - PubMed

Affiliation: Department of Interventional Radiology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.

ABSTRACT
The aim of the current study was to investigate the molecular mechanisms underlying hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) using the expression profiles of HCV-infected Huh7 cells at different time points. The differentially expressed genes (DEGs) were identified with the Samr package in R software once the data were normalized. Functional and pathway enrichment analysis of the identified DEGs was also performed. Subsequently, MCODE in Cytoscape software was applied to conduct module analysis of the constructed co-expression networks. A total of 1,100 DEGs were identified between the HCV-infected and control samples at 12, 18, 24 and 48 h post-infection. DEGs at 24 and 48 h were involved in the same signaling pathways and biological processes, including sterol biosynthetic processes and tRNA amino-acylation. There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h. Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection. In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

Show MeSH
Related in: MedlinePlus