Microarray Profiling of Human Renal Cell Carcinoma: Identification for Potential Biomarkers and Critical Pathways

Aims: The aim of this study was to screen several novel genes associated with renal cell carcinoma (RCC), and analyze the gene functions and signal pathways which were critical to RCCs with DNA microarray. Methods: The gene expression profile of GSE781 was downloaded from Gene Expression Omnibus dat...

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Bibliographic Details
Published in:Kidney & blood pressure research 2013-01, Vol.37 (4-5), p.506-513
Main Authors: Li, Wei, Zhu, Wei, Che, Jianping, Sun, Wei, Liu, Min, Peng, Bo, Zheng, Junhua
Format: Article
Language:English
Subjects:
Biomarkers, Tumor - genetics
Carcinoma, Renal Cell - chemistry
Carcinoma, Renal Cell - genetics
Differentially expressed genes
Female
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks - genetics
Humans
Kidney Neoplasms - chemistry
Kidney Neoplasms - genetics
Male
Microarray profiling
Oligonucleotide Array Sequence Analysis - methods
Original Paper
Renal cell carcinoma
Signal Transduction - genetics
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Summary:Aims: The aim of this study was to screen several novel genes associated with renal cell carcinoma (RCC), and analyze the gene functions and signal pathways which were critical to RCCs with DNA microarray. Methods: The gene expression profile of GSE781 was downloaded from Gene Expression Omnibus database, including 9 RCC samples and 9 healthy controls. Compared with the control samples, differentially expressed genes (DEGs) of RCC was identified the by packages in R. The selected DEGs were further analyzed using bioinformatics methods. Gene ontology (GO) enrichment analysis was performed using Gene Set Analysis Toolkit and protein-protein interaction (PPI) network was constructed with prePPI. Then, pathway enrichment analysis to PPI network was performed using WebGestalt software. Results: A total of 429 DEGs were down-regulated and 418 DEGs were up-regulated in RCC samples compared to healthy controls. A total of 11 remarkable enhanced functions and 13 suppressed functions were identified. PPI nodes of high degrees, such as JAK2, IL8, BMPR2, FN1 and NCR1, were obtained. The DEGs were classified and significantly enriched in cytokine and cytokine receptor pathway. Conclusion: The hub genes we find from RCC samples are not only bio-markers, but also may provide the groundwork for a combination therapy approach for RCCs.
ISSN:1420-4096
1423-0143
DOI:10.1159/000355726