Microarray data analysis of neuroblastoma: Expression of SOX2 downregulates the expression of MYCN

Bao,Juntao; Qin,Luying; Cui,Lingling; Wang,Xiaohui; Meng,Qinglei; Zhu,Linchao; Zhang,Shufeng

doi:10.3892/mmr.2015.4311

Microarray data analysis of neuroblastoma: Expression of SOX2 downregulates the expression of MYCN

Authors:
- Juntao Bao
- Luying Qin
- Lingling Cui
- Xiaohui Wang
- Qinglei Meng
- Linchao Zhu
- Shufeng Zhang
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Affiliations: Department of Pediatric Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China, Nursing College, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
Published online on: September 10, 2015 https://doi.org/10.3892/mmr.2015.4311
Pages: 6867-6872

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Abstract

The present study aimed to identify the genes directly or indirectly correlated with the amplification of MYCN in neuroblastoma (NB). Microarray data (GSE53371) were downloaded from Gene Expression Omnibus, and included 10 NB cell lines with MYCN amplification and 10 NB cell lines with normal MYCN copy numbers. Differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Data package, and a false discovery rate of <0.05 and |log2FC (fold change)|>1 were selected as cut‑off criteria. Hierarchical clustering analysis and Gene Ontology analysis were respectively performed for the DEGs using the Pheatmap package in R language and The Database for Annotation, Visualization and Integrated Discovery. A protein‑protein interaction network (PPI) was constructed for the DEGs using the Search Tool for the Retrieval of Interacting Genes database. Pathway analysis was performed for the DEGs in the PPI network using the WEB‑based GEne SeT AnaLysis Toolkit. The correlation between MYCN and the key gene associated with MYCN was determined using Pearson's correlation coefficient. In total, 137 downregulated and 35 upregulated DEGs were identified. Functional enrichment analysis indicated that KCNMB4 was involved in the regulation of action potential in neuron term, and the FOS, GLI3 and GLI1 genes were involved in the extracellular matrix‑receptor interaction pathway. The PPI network and correlation analysis revealed that the expression of SOX2 was directly correlated with the expression of MYCN, and the correlation coefficient of SOX2 and MYCN was ‑0.83. Therefore, SOX2, KCNMB4, FOS, GLI3 and GLI1 may be involved in the pathogenesis of NB, with the expression of SOX2 downregulating the expression of MYCN.

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