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Published on: June 9, 2020
Transcriptome network analysis reveals candidate genes for renal cell carcinoma
Wei Zhai1, Yun-Fei Xu, Min Liu
1Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
Context:
Renal cell carcinoma (RCC) is a kidney cancer that originates in renal parenchyma and it is the most common type of kidney cancer with approximately 80% lethal cases.
Aims:
To interpret the mechanism, explore the regulation of TF-target genes and TF-pathway, and identify the potential key genes of renal cell carcinoma.
Settings And Design:
After constructing a regulation network from differently expressed genes and transcription factors, pathway regulation network and gene ontology (GO) enrichment analysis were made.
Materials And Methods:
The gene expression profile set GSE6344, a renal cell carcinoma sample set, was collected from NCBI, pathway data from KEGG, and regulationship data from database TRANSFAC and TRED.
Statistical Analysis Used:
Besides different expressed genes obtained by limma, impact analysis method and GO enrichment were applied to find the significant expressed pathways.
Results:
Finally, we constructed a TF-target gene and TF-pathway regulation network of renal cell carcinoma. And some genes proved to be highly related to renal cell carcinoma were identified.
Conclusions:
This study illustrated that by incorporating significantly expressed pathway into a regulation network based analysis, one can derive greater insights into the underlying mechanisms of renal cell carcinoma.
Insights
This study reveals key genes and regulatory networks in renal cell carcinoma (RCC), a deadly kidney cancer. Understanding these mechanisms offers new insights for treating this disease.
Area of Science:
- Oncology
- Bioinformatics
- Molecular Biology
Background:
- Renal cell carcinoma (RCC) is a prevalent and often lethal kidney cancer.
- Approximately 80% of RCC cases are fatal, highlighting the need for better understanding and treatment.
Purpose of the Study:
- To elucidate the underlying mechanisms of renal cell carcinoma (RCC).
- To identify key genes and regulatory pathways involved in RCC development.
- To construct a transcription factor (TF)-target gene and TF-pathway regulation network for RCC.
Main Methods:
- Construction of a regulation network using differentially expressed genes and transcription factors from RCC samples (GSE6344).
- Pathway analysis using KEGG data and regulatory relationships from TRANSFAC and TRED databases.
- Gene Ontology (GO) enrichment analysis and impact analysis to identify significant pathways.
Main Results:
- A comprehensive TF-target gene and TF-pathway regulation network for renal cell carcinoma was successfully constructed.
- Several key genes significantly related to renal cell carcinoma were identified through the analysis.
Conclusions:
- Integrating pathway analysis into regulation network studies provides deeper insights into RCC mechanisms.
- The identified key genes and networks offer potential targets for future renal cell carcinoma research and therapeutic strategies.
